202406_New_pareto_front_calculation_allHormones
This is a new pareto-front calculation for all hormone assays I performed for RSA. I started to plot all hormones into one plot but it was too noisy. So I decided to plot each hormone/experiment separately, for both control and salt stress, day 9 only.
getwd()## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/202406_new_pareto_calculation_all_hormones"list.files(pattern=".csv")## [1] "ABA-only.csv"
## [2] "ACC-only-d5excluded.csv"
## [3] "ACC-only.csv"
## [4] "cyto-only.csv"
## [5] "GA-only-d5excluded.csv"
## [6] "GA-only.csv"
## [7] "IAA-only-d5excluded.csv"
## [8] "IAA-only.csv"
## [9] "point_similarity_maryamModified.csv"
## [10] "point_similarity_maryamModified_control_Removed.csv"all_data <- read.csv("point_similarity_maryamModified_control_Removed.csv")
all_dataall_data$All.condition<-paste(all_data$Condition1,all_data$Condition2, sep="+")
all_dataall_data$All.ID2<-paste(all_data$Accession,all_data$All.condition, all_data$Day,sep="_")
all_dataall_data2 <- subset(all_data, all_data$Day > 5)library(ggplot2)
library(ggpubr)
library(multcompView)## Warning: package 'multcompView' was built under R version 4.3.2aov(Distance.squared ~ All.ID2, data = all_data2)## Call:
## aov(formula = Distance.squared ~ All.ID2, data = all_data2)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 992357.5 1652927.0
## Deg. of Freedom 29 353
##
## Residual standard error: 68.42889
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Distance.squared ~ All.ID2, data = all_data2))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Distance.squared ~ All.ID2, data = all_data2)
##
## $All.ID2
## diff lwr upr
## LA1511_S+hiacc_9-LA1511_S+hiaba_9 1.291650e+00 -148.0603488 150.643649
## LA1511_S+hicyto_9-LA1511_S+hiaba_9 8.745611e-03 -136.3303526 136.347844
## LA1511_S+higa_9-LA1511_S+hiaba_9 1.679413e+01 -114.4936108 148.081862
## LA1511_S+iaa_9-LA1511_S+hiaba_9 4.314346e+00 -132.0247518 140.653445
## LA1511_S+lowaba_9-LA1511_S+hiaba_9 3.389756e-01 -133.2455134 133.923465
## LA1511_S+lowacc_9-LA1511_S+hiaba_9 4.810717e-02 -149.3038920 149.400106
## LA1511_S+lowcyto_9-LA1511_S+hiaba_9 3.466717e-02 -136.3044311 136.373765
## LA1511_S+lowga_9-LA1511_S+hiaba_9 1.392044e+00 -129.8956927 132.679780
## LA1511_S+only_9-LA1511_S+hiaba_9 7.019147e+00 -105.7161352 119.754428
## M058_S+hiaba_9-LA1511_S+hiaba_9 3.596850e-01 -139.3463177 140.065688
## M058_S+hiacc_9-LA1511_S+hiaba_9 5.687039e-01 -133.0157851 134.153193
## M058_S+hicyto_9-LA1511_S+hiaba_9 3.039221e-02 -139.6756105 139.736395
## M058_S+higa_9-LA1511_S+hiaba_9 2.609399e+00 -130.9750898 136.193888
## M058_S+iaa_9-LA1511_S+hiaba_9 4.533236e+00 -129.0512527 138.117725
## M058_S+lowaba_9-LA1511_S+hiaba_9 3.836969e-01 -133.2007921 133.968186
## M058_S+lowacc_9-LA1511_S+hiaba_9 1.494052e+00 -132.0904374 135.078541
## M058_S+lowcyto_9-LA1511_S+hiaba_9 5.251553e-02 -133.5319735 133.637005
## M058_S+lowga_9-LA1511_S+hiaba_9 5.827359e+00 -127.7571299 139.411848
## M058_S+only_9-LA1511_S+hiaba_9 2.319020e+00 -110.4162620 115.054302
## M248_S+hiaba_9-LA1511_S+hiaba_9 2.866727e+00 -133.4723713 139.205825
## M248_S+hiacc_9-LA1511_S+hiaba_9 3.549289e+00 -130.0352000 137.133778
## M248_S+hicyto_9-LA1511_S+hiaba_9 1.483471e-02 -139.6911680 139.720837
## M248_S+higa_9-LA1511_S+hiaba_9 1.355693e+02 1.9848079 269.153786
## M248_S+iaa_9-LA1511_S+hiaba_9 6.133729e+00 -127.4507599 139.718218
## M248_S+lowaba_9-LA1511_S+hiaba_9 8.260620e+00 -125.3238686 141.845109
## M248_S+lowacc_9-LA1511_S+hiaba_9 9.859692e+00 -126.4794059 146.198791
## M248_S+lowcyto_9-LA1511_S+hiaba_9 1.613536e-01 -136.1777446 136.500452
## M248_S+lowga_9-LA1511_S+hiaba_9 2.968668e+02 163.2822679 430.451246
## M248_S+only_9-LA1511_S+hiaba_9 2.916361e+01 -82.7233191 141.050535
## LA1511_S+hicyto_9-LA1511_S+hiacc_9 -1.282905e+00 -137.6220029 135.056194
## LA1511_S+higa_9-LA1511_S+hiacc_9 1.550248e+01 -115.7852612 146.790212
## LA1511_S+iaa_9-LA1511_S+hiacc_9 3.022696e+00 -133.3164022 139.361794
## LA1511_S+lowaba_9-LA1511_S+hiacc_9 -9.526747e-01 -134.5371638 132.631814
## LA1511_S+lowacc_9-LA1511_S+hiacc_9 -1.243543e+00 -150.5955423 148.108456
## LA1511_S+lowcyto_9-LA1511_S+hiacc_9 -1.256983e+00 -137.5960814 135.082115
## LA1511_S+lowga_9-LA1511_S+hiacc_9 1.003933e-01 -131.1873431 131.388130
## LA1511_S+only_9-LA1511_S+hiacc_9 5.727496e+00 -107.0077855 118.462778
## M058_S+hiaba_9-LA1511_S+hiacc_9 -9.319654e-01 -140.6379681 138.774037
## M058_S+hiacc_9-LA1511_S+hiacc_9 -7.229464e-01 -134.3074355 132.861543
## M058_S+hicyto_9-LA1511_S+hiacc_9 -1.261258e+00 -140.9672608 138.444745
## M058_S+higa_9-LA1511_S+hiacc_9 1.317749e+00 -132.2667402 134.902238
## M058_S+iaa_9-LA1511_S+hiacc_9 3.241586e+00 -130.3429031 136.826075
## M058_S+lowaba_9-LA1511_S+hiacc_9 -9.079534e-01 -134.4924425 132.676536
## M058_S+lowacc_9-LA1511_S+hiacc_9 2.024013e-01 -133.3820878 133.786890
## M058_S+lowcyto_9-LA1511_S+hiacc_9 -1.239135e+00 -134.8236239 132.345354
## M058_S+lowga_9-LA1511_S+hiacc_9 4.535709e+00 -129.0487803 138.120198
## M058_S+only_9-LA1511_S+hiacc_9 1.027369e+00 -111.7079123 113.762651
## M248_S+hiaba_9-LA1511_S+hiacc_9 1.575077e+00 -134.7640216 137.914175
## M248_S+hiacc_9-LA1511_S+hiacc_9 2.257639e+00 -131.3268504 135.842128
## M248_S+hicyto_9-LA1511_S+hiacc_9 -1.276816e+00 -140.9828183 138.429187
## M248_S+higa_9-LA1511_S+hiacc_9 1.342776e+02 0.6931575 267.862136
## M248_S+iaa_9-LA1511_S+hiacc_9 4.842079e+00 -128.7424103 138.426568
## M248_S+lowaba_9-LA1511_S+hiacc_9 6.968970e+00 -126.6155190 140.553459
## M248_S+lowacc_9-LA1511_S+hiacc_9 8.568042e+00 -127.7710563 144.907140
## M248_S+lowcyto_9-LA1511_S+hiacc_9 -1.130297e+00 -137.4693949 135.208802
## M248_S+lowga_9-LA1511_S+hiacc_9 2.955751e+02 161.9906175 429.159596
## M248_S+only_9-LA1511_S+hiacc_9 2.787196e+01 -84.0149695 139.758885
## LA1511_S+higa_9-LA1511_S+hicyto_9 1.678538e+01 -99.4849937 133.055754
## LA1511_S+iaa_9-LA1511_S+hicyto_9 4.305601e+00 -117.6397959 126.250997
## LA1511_S+lowaba_9-LA1511_S+hicyto_9 3.302300e-01 -118.5274402 119.187900
## LA1511_S+lowacc_9-LA1511_S+hicyto_9 3.936156e-02 -136.2997367 136.378460
## LA1511_S+lowcyto_9-LA1511_S+hicyto_9 2.592156e-02 -121.9194751 121.971318
## LA1511_S+lowga_9-LA1511_S+hicyto_9 1.383298e+00 -114.8870756 117.653672
## LA1511_S+only_9-LA1511_S+hicyto_9 7.010401e+00 -87.8135085 101.834310
## M058_S+hiaba_9-LA1511_S+hicyto_9 3.509393e-01 -125.3474984 126.049377
## M058_S+hiacc_9-LA1511_S+hicyto_9 5.599583e-01 -118.2977119 119.417629
## M058_S+hicyto_9-LA1511_S+hicyto_9 2.164660e-02 -125.6767911 125.720084
## M058_S+higa_9-LA1511_S+hicyto_9 2.600654e+00 -116.2570166 121.458324
## M058_S+iaa_9-LA1511_S+hicyto_9 4.524491e+00 -114.3331795 123.382161
## M058_S+lowaba_9-LA1511_S+hicyto_9 3.749513e-01 -118.4827189 119.232622
## M058_S+lowacc_9-LA1511_S+hicyto_9 1.485306e+00 -117.3723642 120.342976
## M058_S+lowcyto_9-LA1511_S+hicyto_9 4.376992e-02 -118.8139003 118.901440
## M058_S+lowga_9-LA1511_S+hicyto_9 5.818614e+00 -113.0390567 124.676284
## M058_S+only_9-LA1511_S+hicyto_9 2.310274e+00 -92.5136353 97.134184
## M248_S+hiaba_9-LA1511_S+hicyto_9 2.857981e+00 -119.0874153 124.803378
## M248_S+hiacc_9-LA1511_S+hicyto_9 3.540543e+00 -115.3171268 122.398214
## M248_S+hicyto_9-LA1511_S+hicyto_9 6.089097e-03 -125.6923486 125.704527
## M248_S+higa_9-LA1511_S+hicyto_9 1.355606e+02 16.7028811 254.418222
## M248_S+iaa_9-LA1511_S+hicyto_9 6.124984e+00 -112.7326867 124.982654
## M248_S+lowaba_9-LA1511_S+hicyto_9 8.251875e+00 -110.6057954 127.109545
## M248_S+lowacc_9-LA1511_S+hicyto_9 9.850947e+00 -112.0944500 131.796343
## M248_S+lowcyto_9-LA1511_S+hicyto_9 1.526080e-01 -121.7927887 122.098005
## M248_S+lowga_9-LA1511_S+hicyto_9 2.968580e+02 178.0003411 415.715682
## M248_S+only_9-LA1511_S+hicyto_9 2.915486e+01 -64.6588601 122.968585
## LA1511_S+iaa_9-LA1511_S+higa_9 -1.247978e+01 -128.7501528 103.790594
## LA1511_S+lowaba_9-LA1511_S+higa_9 -1.645515e+01 -129.4828713 96.572571
## LA1511_S+lowacc_9-LA1511_S+higa_9 -1.674602e+01 -148.0337548 114.541718
## LA1511_S+lowcyto_9-LA1511_S+higa_9 -1.675946e+01 -133.0298320 99.510915
## LA1511_S+lowga_9-LA1511_S+higa_9 -1.540208e+01 -125.7058434 94.901680
## LA1511_S+only_9-LA1511_S+higa_9 -9.774979e+00 -97.1803211 77.630363
## M058_S+hiaba_9-LA1511_S+higa_9 -1.643444e+01 -136.6351780 103.766297
## M058_S+hiacc_9-LA1511_S+higa_9 -1.622542e+01 -129.2531430 96.802300
## M058_S+hicyto_9-LA1511_S+higa_9 -1.676373e+01 -136.9644707 103.437004
## M058_S+higa_9-LA1511_S+higa_9 -1.418473e+01 -127.2124477 98.842995
## M058_S+iaa_9-LA1511_S+higa_9 -1.226089e+01 -125.2886106 100.766832
## M058_S+lowaba_9-LA1511_S+higa_9 -1.641043e+01 -129.4381500 96.617293
## M058_S+lowacc_9-LA1511_S+higa_9 -1.530007e+01 -128.3277953 97.727647
## M058_S+lowcyto_9-LA1511_S+higa_9 -1.674161e+01 -129.7693314 96.286111
## M058_S+lowga_9-LA1511_S+higa_9 -1.096677e+01 -123.9944878 102.060955
## M058_S+only_9-LA1511_S+higa_9 -1.447511e+01 -101.8804479 72.930236
## M248_S+hiaba_9-LA1511_S+higa_9 -1.392740e+01 -130.1977723 102.342975
## M248_S+hiacc_9-LA1511_S+higa_9 -1.324484e+01 -126.2725579 99.782885
## M248_S+hicyto_9-LA1511_S+higa_9 -1.677929e+01 -136.9800282 103.421447
## M248_S+higa_9-LA1511_S+higa_9 1.187752e+02 5.7474500 231.802893
## M248_S+iaa_9-LA1511_S+higa_9 -1.066040e+01 -123.6881178 102.367325
## M248_S+lowaba_9-LA1511_S+higa_9 -8.533505e+00 -121.5612265 104.494216
## M248_S+lowacc_9-LA1511_S+higa_9 -6.934433e+00 -123.2048069 109.335940
## M248_S+lowcyto_9-LA1511_S+higa_9 -1.663277e+01 -132.9031456 99.637602
## M248_S+lowga_9-LA1511_S+higa_9 2.800726e+02 167.0449100 393.100353
## M248_S+only_9-LA1511_S+higa_9 1.236948e+01 -73.9388865 98.677852
## LA1511_S+lowaba_9-LA1511_S+iaa_9 -3.975371e+00 -122.8330410 114.882299
## LA1511_S+lowacc_9-LA1511_S+iaa_9 -4.266239e+00 -140.6053374 132.072859
## LA1511_S+lowcyto_9-LA1511_S+iaa_9 -4.279679e+00 -126.2250759 117.665717
## LA1511_S+lowga_9-LA1511_S+iaa_9 -2.922303e+00 -119.1926764 113.348071
## LA1511_S+only_9-LA1511_S+iaa_9 2.704800e+00 -92.1191093 97.528710
## M058_S+hiaba_9-LA1511_S+iaa_9 -3.954661e+00 -129.6530992 121.743776
## M058_S+hiacc_9-LA1511_S+iaa_9 -3.745642e+00 -122.6033127 115.112028
## M058_S+hicyto_9-LA1511_S+iaa_9 -4.283954e+00 -129.9823919 121.414484
## M058_S+higa_9-LA1511_S+iaa_9 -1.704947e+00 -120.5626174 117.152723
## M058_S+iaa_9-LA1511_S+iaa_9 2.188899e-01 -118.6387803 119.076560
## M058_S+lowaba_9-LA1511_S+iaa_9 -3.930649e+00 -122.7883197 114.927021
## M058_S+lowacc_9-LA1511_S+iaa_9 -2.820295e+00 -121.6779650 116.037375
## M058_S+lowcyto_9-LA1511_S+iaa_9 -4.261831e+00 -123.1195011 114.595839
## M058_S+lowga_9-LA1511_S+iaa_9 1.513013e+00 -117.3446575 120.370683
## M058_S+only_9-LA1511_S+iaa_9 -1.995327e+00 -96.8192361 92.828583
## M248_S+hiaba_9-LA1511_S+iaa_9 -1.447619e+00 -123.3930161 120.497777
## M248_S+hiacc_9-LA1511_S+iaa_9 -7.650574e-01 -119.6227276 118.092613
## M248_S+hicyto_9-LA1511_S+iaa_9 -4.299512e+00 -129.9979494 121.398926
## M248_S+higa_9-LA1511_S+iaa_9 1.312550e+02 12.3972803 250.112621
## M248_S+iaa_9-LA1511_S+iaa_9 1.819383e+00 -117.0382875 120.677053
## M248_S+lowaba_9-LA1511_S+iaa_9 3.946274e+00 -114.9113962 122.803944
## M248_S+lowacc_9-LA1511_S+iaa_9 5.545346e+00 -116.4000508 127.490743
## M248_S+lowcyto_9-LA1511_S+iaa_9 -4.152993e+00 -126.0983894 117.792404
## M248_S+lowga_9-LA1511_S+iaa_9 2.925524e+02 173.6947403 411.410081
## M248_S+only_9-LA1511_S+iaa_9 2.484926e+01 -68.9644609 118.662984
## LA1511_S+lowacc_9-LA1511_S+lowaba_9 -2.908685e-01 -133.8753575 133.293621
## LA1511_S+lowcyto_9-LA1511_S+lowaba_9 -3.043085e-01 -119.1619787 118.553362
## LA1511_S+lowga_9-LA1511_S+lowaba_9 1.053068e+00 -111.9746533 114.080789
## LA1511_S+only_9-LA1511_S+lowaba_9 6.680171e+00 -84.1385486 97.498890
## M058_S+hiaba_9-LA1511_S+lowaba_9 2.070932e-02 -122.6844791 122.725898
## M058_S+hiacc_9-LA1511_S+lowaba_9 2.297283e-01 -115.4578328 115.917289
## M058_S+hicyto_9-LA1511_S+lowaba_9 -3.085834e-01 -123.0137718 122.396605
## M058_S+higa_9-LA1511_S+lowaba_9 2.270424e+00 -113.4171375 117.957985
## M058_S+iaa_9-LA1511_S+lowaba_9 4.194261e+00 -111.4933004 119.881822
## M058_S+lowaba_9-LA1511_S+lowaba_9 4.472130e-02 -115.6428398 115.732282
## M058_S+lowacc_9-LA1511_S+lowaba_9 1.155076e+00 -114.5324851 116.842637
## M058_S+lowcyto_9-LA1511_S+lowaba_9 -2.864601e-01 -115.9740212 115.401101
## M058_S+lowga_9-LA1511_S+lowaba_9 5.488384e+00 -110.1991776 121.175945
## M058_S+only_9-LA1511_S+lowaba_9 1.980044e+00 -88.8386754 92.798764
## M248_S+hiaba_9-LA1511_S+lowaba_9 2.527751e+00 -116.3299189 121.385422
## M248_S+hiacc_9-LA1511_S+lowaba_9 3.210313e+00 -112.4772477 118.897874
## M248_S+hicyto_9-LA1511_S+lowaba_9 -3.241409e-01 -123.0293293 122.381047
## M248_S+higa_9-LA1511_S+lowaba_9 1.352303e+02 19.5427602 250.917882
## M248_S+iaa_9-LA1511_S+lowaba_9 5.794753e+00 -109.8928076 121.482315
## M248_S+lowaba_9-LA1511_S+lowaba_9 7.921645e+00 -107.7659163 123.609206
## M248_S+lowacc_9-LA1511_S+lowaba_9 9.520717e+00 -109.3369536 128.378387
## M248_S+lowcyto_9-LA1511_S+lowaba_9 -1.776220e-01 -119.0352923 118.680048
## M248_S+lowga_9-LA1511_S+lowaba_9 2.965278e+02 180.8402202 412.215342
## M248_S+only_9-LA1511_S+lowaba_9 2.882463e+01 -60.9388376 118.588103
## LA1511_S+lowcyto_9-LA1511_S+lowacc_9 -1.344000e-02 -136.3525382 136.325658
## LA1511_S+lowga_9-LA1511_S+lowacc_9 1.343936e+00 -129.9437999 132.631673
## LA1511_S+only_9-LA1511_S+lowacc_9 6.971039e+00 -105.7642424 119.706321
## M058_S+hiaba_9-LA1511_S+lowacc_9 3.115778e-01 -139.3944249 140.017580
## M058_S+hiacc_9-LA1511_S+lowacc_9 5.205968e-01 -133.0638923 134.105086
## M058_S+hicyto_9-LA1511_S+lowacc_9 -1.771496e-02 -139.7237177 139.688288
## M058_S+higa_9-LA1511_S+lowacc_9 2.561292e+00 -131.0231970 136.145781
## M058_S+iaa_9-LA1511_S+lowacc_9 4.485129e+00 -129.0993599 138.069618
## M058_S+lowaba_9-LA1511_S+lowacc_9 3.355898e-01 -133.2488993 133.920079
## M058_S+lowacc_9-LA1511_S+lowacc_9 1.445944e+00 -132.1385446 135.030434
## M058_S+lowcyto_9-LA1511_S+lowacc_9 4.408367e-03 -133.5800807 133.588897
## M058_S+lowga_9-LA1511_S+lowacc_9 5.779252e+00 -127.8052371 139.363741
## M058_S+only_9-LA1511_S+lowacc_9 2.270913e+00 -110.4643691 115.006194
## M248_S+hiaba_9-LA1511_S+lowacc_9 2.818620e+00 -133.5204784 139.157718
## M248_S+hiacc_9-LA1511_S+lowacc_9 3.501182e+00 -130.0833072 137.085671
## M248_S+hicyto_9-LA1511_S+lowacc_9 -3.327246e-02 -139.7392752 139.672730
## M248_S+higa_9-LA1511_S+lowacc_9 1.355212e+02 1.9367007 269.105679
## M248_S+iaa_9-LA1511_S+lowacc_9 6.085622e+00 -127.4988671 139.670111
## M248_S+lowaba_9-LA1511_S+lowacc_9 8.212513e+00 -125.3719758 141.797002
## M248_S+lowacc_9-LA1511_S+lowacc_9 9.811585e+00 -126.5275131 146.150683
## M248_S+lowcyto_9-LA1511_S+lowacc_9 1.132464e-01 -136.2258518 136.452345
## M248_S+lowga_9-LA1511_S+lowacc_9 2.968186e+02 163.2341607 430.403139
## M248_S+only_9-LA1511_S+lowacc_9 2.911550e+01 -82.7714263 141.002428
## LA1511_S+lowga_9-LA1511_S+lowcyto_9 1.357376e+00 -114.9129972 117.627750
## LA1511_S+only_9-LA1511_S+lowcyto_9 6.984479e+00 -87.8394301 101.808389
## M058_S+hiaba_9-LA1511_S+lowcyto_9 3.250178e-01 -125.3734199 126.023456
## M058_S+hiacc_9-LA1511_S+lowcyto_9 5.340368e-01 -118.3236335 119.391707
## M058_S+hicyto_9-LA1511_S+lowcyto_9 -4.274958e-03 -125.7027127 125.694163
## M058_S+higa_9-LA1511_S+lowcyto_9 2.574732e+00 -116.2829382 121.432402
## M058_S+iaa_9-LA1511_S+lowcyto_9 4.498569e+00 -114.3591011 123.356239
## M058_S+lowaba_9-LA1511_S+lowcyto_9 3.490298e-01 -118.5086405 119.206700
## M058_S+lowacc_9-LA1511_S+lowcyto_9 1.459384e+00 -117.3982858 120.317055
## M058_S+lowcyto_9-LA1511_S+lowcyto_9 1.784837e-02 -118.8398219 118.875519
## M058_S+lowga_9-LA1511_S+lowcyto_9 5.792692e+00 -113.0649783 124.650362
## M058_S+only_9-LA1511_S+lowcyto_9 2.284353e+00 -92.5395569 97.108262
## M248_S+hiaba_9-LA1511_S+lowcyto_9 2.832060e+00 -119.1133369 124.777456
## M248_S+hiacc_9-LA1511_S+lowcyto_9 3.514622e+00 -115.3430484 122.372292
## M248_S+hicyto_9-LA1511_S+lowcyto_9 -1.983246e-02 -125.7182702 125.678605
## M248_S+higa_9-LA1511_S+lowcyto_9 1.355346e+02 16.6769595 254.392300
## M248_S+iaa_9-LA1511_S+lowcyto_9 6.099062e+00 -112.7586083 124.956732
## M248_S+lowaba_9-LA1511_S+lowcyto_9 8.225953e+00 -110.6317170 127.083624
## M248_S+lowacc_9-LA1511_S+lowcyto_9 9.825025e+00 -112.1203715 131.770422
## M248_S+lowcyto_9-LA1511_S+lowcyto_9 1.266864e-01 -121.8187102 122.072083
## M248_S+lowga_9-LA1511_S+lowcyto_9 2.968321e+02 177.9744195 415.689760
## M248_S+only_9-LA1511_S+lowcyto_9 2.912894e+01 -64.6847817 122.942664
## LA1511_S+only_9-LA1511_S+lowga_9 5.627103e+00 -81.7782392 93.032445
## M058_S+hiaba_9-LA1511_S+lowga_9 -1.032359e+00 -121.2330961 119.168379
## M058_S+hiacc_9-LA1511_S+lowga_9 -8.233397e-01 -113.8510611 112.204382
## M058_S+hicyto_9-LA1511_S+lowga_9 -1.361651e+00 -121.5623888 118.839086
## M058_S+higa_9-LA1511_S+lowga_9 1.217356e+00 -111.8103658 114.245077
## M058_S+iaa_9-LA1511_S+lowga_9 3.141193e+00 -109.8865287 116.168914
## M058_S+lowaba_9-LA1511_S+lowga_9 -1.008347e+00 -114.0360681 112.019375
## M058_S+lowacc_9-LA1511_S+lowga_9 1.020080e-01 -112.9257134 113.129729
## M058_S+lowcyto_9-LA1511_S+lowga_9 -1.339528e+00 -114.3672495 111.688193
## M058_S+lowga_9-LA1511_S+lowga_9 4.435315e+00 -108.5924059 117.463037
## M058_S+only_9-LA1511_S+lowga_9 9.269761e-01 -86.4783660 88.332318
## M248_S+hiaba_9-LA1511_S+lowga_9 1.474683e+00 -114.7956903 117.745057
## M248_S+hiacc_9-LA1511_S+lowga_9 2.157245e+00 -110.8704760 115.184967
## M248_S+hicyto_9-LA1511_S+lowga_9 -1.377209e+00 -121.5779463 118.823528
## M248_S+higa_9-LA1511_S+lowga_9 1.341773e+02 21.1495319 247.204975
## M248_S+iaa_9-LA1511_S+lowga_9 4.741685e+00 -108.2860359 117.769407
## M248_S+lowaba_9-LA1511_S+lowga_9 6.868577e+00 -106.1591446 119.896298
## M248_S+lowacc_9-LA1511_S+lowga_9 8.467649e+00 -107.8027250 124.738022
## M248_S+lowcyto_9-LA1511_S+lowga_9 -1.230690e+00 -117.5010637 115.039684
## M248_S+lowga_9-LA1511_S+lowga_9 2.954747e+02 182.4469919 408.502435
## M248_S+only_9-LA1511_S+lowga_9 2.777156e+01 -58.5368046 114.079934
## M058_S+hiaba_9-LA1511_S+only_9 -6.659462e+00 -106.2636347 92.944711
## M058_S+hiacc_9-LA1511_S+only_9 -6.450443e+00 -97.2691622 84.368277
## M058_S+hicyto_9-LA1511_S+only_9 -6.988754e+00 -106.5929274 92.615419
## M058_S+higa_9-LA1511_S+only_9 -4.409747e+00 -95.2284669 86.408972
## M058_S+iaa_9-LA1511_S+only_9 -2.485910e+00 -93.3046298 88.332809
## M058_S+lowaba_9-LA1511_S+only_9 -6.635450e+00 -97.4541692 84.183270
## M058_S+lowacc_9-LA1511_S+only_9 -5.525095e+00 -96.3438145 85.293625
## M058_S+lowcyto_9-LA1511_S+only_9 -6.966631e+00 -97.7853506 83.852089
## M058_S+lowga_9-LA1511_S+only_9 -1.191787e+00 -92.0105070 89.626932
## M058_S+only_9-LA1511_S+only_9 -4.700127e+00 -60.4896227 51.089369
## M248_S+hiaba_9-LA1511_S+only_9 -4.152420e+00 -98.9763291 90.671490
## M248_S+hiacc_9-LA1511_S+only_9 -3.469858e+00 -94.2885771 87.348862
## M248_S+hicyto_9-LA1511_S+only_9 -7.004312e+00 -106.6084849 92.599861
## M248_S+higa_9-LA1511_S+only_9 1.285502e+02 37.7314308 219.368870
## M248_S+iaa_9-LA1511_S+only_9 -8.854174e-01 -91.7041370 89.933302
## M248_S+lowaba_9-LA1511_S+only_9 1.241474e+00 -89.5772457 92.060193
## M248_S+lowacc_9-LA1511_S+only_9 2.840546e+00 -91.9833638 97.664455
## M248_S+lowcyto_9-LA1511_S+only_9 -6.857793e+00 -101.6817024 87.966117
## M248_S+lowga_9-LA1511_S+only_9 2.898476e+02 199.0288908 380.666330
## M248_S+only_9-LA1511_S+only_9 2.214446e+01 -31.9102200 76.199143
## M058_S+hiacc_9-M058_S+hiaba_9 2.090190e-01 -122.4961694 122.914207
## M058_S+hicyto_9-M058_S+hiaba_9 -3.292928e-01 -129.6719181 129.013333
## M058_S+higa_9-M058_S+hiaba_9 2.249714e+00 -120.4554741 124.954903
## M058_S+iaa_9-M058_S+hiaba_9 4.173551e+00 -118.5316370 126.878740
## M058_S+lowaba_9-M058_S+hiaba_9 2.401198e-02 -122.6811764 122.729200
## M058_S+lowacc_9-M058_S+hiaba_9 1.134367e+00 -121.5708217 123.839555
## M058_S+lowcyto_9-M058_S+hiaba_9 -3.071694e-01 -123.0123578 122.398019
## M058_S+lowga_9-M058_S+hiaba_9 5.467674e+00 -117.2375142 128.172863
## M058_S+only_9-M058_S+hiaba_9 1.959335e+00 -97.6448383 101.563508
## M248_S+hiaba_9-M058_S+hiaba_9 2.507042e+00 -123.1913958 128.205480
## M248_S+hiacc_9-M058_S+hiaba_9 3.189604e+00 -119.5155843 125.894792
## M248_S+hicyto_9-M058_S+hiaba_9 -3.448503e-01 -129.6874756 128.997775
## M248_S+higa_9-M058_S+hiaba_9 1.352096e+02 12.5044236 257.914800
## M248_S+iaa_9-M058_S+hiaba_9 5.774044e+00 -116.9311442 128.479233
## M248_S+lowaba_9-M058_S+hiaba_9 7.900935e+00 -114.8042529 130.606124
## M248_S+lowacc_9-M058_S+hiaba_9 9.500007e+00 -116.1984304 135.198445
## M248_S+lowcyto_9-M058_S+hiaba_9 -1.983313e-01 -125.8967691 125.500106
## M248_S+lowga_9-M058_S+hiaba_9 2.965071e+02 173.8018836 419.212260
## M248_S+only_9-M058_S+hiaba_9 2.880392e+01 -69.8390291 127.446875
## M058_S+hicyto_9-M058_S+hiacc_9 -5.383117e-01 -123.2435001 122.166877
## M058_S+higa_9-M058_S+hiacc_9 2.040695e+00 -113.6468658 117.728256
## M058_S+iaa_9-M058_S+hiacc_9 3.964532e+00 -111.7230287 119.652093
## M058_S+lowaba_9-M058_S+hiacc_9 -1.850070e-01 -115.8725681 115.502554
## M058_S+lowacc_9-M058_S+hiacc_9 9.253477e-01 -114.7622134 116.612909
## M058_S+lowcyto_9-M058_S+hiacc_9 -5.161884e-01 -116.2037495 115.171373
## M058_S+lowga_9-M058_S+hiacc_9 5.258655e+00 -110.4289059 120.946216
## M058_S+only_9-M058_S+hiacc_9 1.750316e+00 -89.0684037 92.569035
## M248_S+hiaba_9-M058_S+hiacc_9 2.298023e+00 -116.5596472 121.155693
## M248_S+hiacc_9-M058_S+hiacc_9 2.980585e+00 -112.7069760 118.668146
## M248_S+hicyto_9-M058_S+hiacc_9 -5.538692e-01 -123.2590576 122.151319
## M248_S+higa_9-M058_S+hiacc_9 1.350006e+02 19.3130319 250.688154
## M248_S+iaa_9-M058_S+hiacc_9 5.565025e+00 -110.1225359 121.252586
## M248_S+lowaba_9-M058_S+hiacc_9 7.691917e+00 -107.9956446 123.379478
## M248_S+lowacc_9-M058_S+hiacc_9 9.290988e+00 -109.5666819 128.148659
## M248_S+lowcyto_9-M058_S+hiacc_9 -4.073503e-01 -119.2650206 118.450320
## M248_S+lowga_9-M058_S+hiacc_9 2.962981e+02 180.6104919 411.985614
## M248_S+only_9-M058_S+hiacc_9 2.859490e+01 -61.1685659 118.358374
## M058_S+higa_9-M058_S+hicyto_9 2.579007e+00 -120.1261814 125.284195
## M058_S+iaa_9-M058_S+hicyto_9 4.502844e+00 -118.2023443 127.208033
## M058_S+lowaba_9-M058_S+hicyto_9 3.533047e-01 -122.3518837 123.058493
## M058_S+lowacc_9-M058_S+hicyto_9 1.463659e+00 -121.2415290 124.168848
## M058_S+lowcyto_9-M058_S+hicyto_9 2.212333e-02 -122.6830651 122.727312
## M058_S+lowga_9-M058_S+hicyto_9 5.796967e+00 -116.9082215 128.502155
## M058_S+only_9-M058_S+hicyto_9 2.288628e+00 -97.3155455 101.892801
## M248_S+hiaba_9-M058_S+hicyto_9 2.836335e+00 -122.8621030 128.534772
## M248_S+hiacc_9-M058_S+hicyto_9 3.518897e+00 -119.1862916 126.224085
## M248_S+hicyto_9-M058_S+hicyto_9 -1.555750e-02 -129.3581829 129.327068
## M248_S+higa_9-M058_S+hicyto_9 1.355389e+02 12.8337163 258.244093
## M248_S+iaa_9-M058_S+hicyto_9 6.103337e+00 -116.6018515 128.808525
## M248_S+lowaba_9-M058_S+hicyto_9 8.230228e+00 -114.4749602 130.935417
## M248_S+lowacc_9-M058_S+hicyto_9 9.829300e+00 -115.8691377 135.527738
## M248_S+lowcyto_9-M058_S+hicyto_9 1.309614e-01 -125.5674763 125.829399
## M248_S+lowga_9-M058_S+hicyto_9 2.968364e+02 174.1311763 419.541553
## M248_S+only_9-M058_S+hicyto_9 2.913322e+01 -69.5097364 127.776168
## M058_S+iaa_9-M058_S+higa_9 1.923837e+00 -113.7637240 117.611398
## M058_S+lowaba_9-M058_S+higa_9 -2.225702e+00 -117.9132634 113.461859
## M058_S+lowacc_9-M058_S+higa_9 -1.115348e+00 -116.8029087 114.572213
## M058_S+lowcyto_9-M058_S+higa_9 -2.556884e+00 -118.2444448 113.130677
## M058_S+lowga_9-M058_S+higa_9 3.217960e+00 -112.4696012 118.905521
## M058_S+only_9-M058_S+higa_9 -2.903794e-01 -91.1090990 90.528340
## M248_S+hiaba_9-M058_S+higa_9 2.573277e-01 -118.6003425 119.114998
## M248_S+hiacc_9-M058_S+higa_9 9.398898e-01 -114.7476713 116.627451
## M248_S+hicyto_9-M058_S+higa_9 -2.594565e+00 -125.2997529 120.110624
## M248_S+higa_9-M058_S+higa_9 1.329599e+02 17.2723366 248.647459
## M248_S+iaa_9-M058_S+higa_9 3.524330e+00 -112.1632312 119.211891
## M248_S+lowaba_9-M058_S+higa_9 5.651221e+00 -110.0363399 121.338782
## M248_S+lowacc_9-M058_S+higa_9 7.250293e+00 -111.6073772 126.107963
## M248_S+lowcyto_9-M058_S+higa_9 -2.448046e+00 -121.3057159 116.409625
## M248_S+lowga_9-M058_S+higa_9 2.942574e+02 178.5697966 409.944919
## M248_S+only_9-M058_S+higa_9 2.655421e+01 -63.2092612 116.317679
## M058_S+lowaba_9-M058_S+iaa_9 -4.149539e+00 -119.8371005 111.538022
## M058_S+lowacc_9-M058_S+iaa_9 -3.039185e+00 -118.7267458 112.648376
## M058_S+lowcyto_9-M058_S+iaa_9 -4.480721e+00 -120.1682819 111.206840
## M058_S+lowga_9-M058_S+iaa_9 1.294123e+00 -114.3934383 116.981684
## M058_S+only_9-M058_S+iaa_9 -2.214217e+00 -93.0329361 88.604503
## M248_S+hiaba_9-M058_S+iaa_9 -1.666509e+00 -120.5241796 117.191161
## M248_S+hiacc_9-M058_S+iaa_9 -9.839473e-01 -116.6715084 114.703614
## M248_S+hicyto_9-M058_S+iaa_9 -4.518402e+00 -127.2235900 118.186787
## M248_S+higa_9-M058_S+iaa_9 1.310361e+02 15.3484995 246.723622
## M248_S+iaa_9-M058_S+iaa_9 1.600493e+00 -114.0870683 117.288054
## M248_S+lowaba_9-M058_S+iaa_9 3.727384e+00 -111.9601770 119.414945
## M248_S+lowacc_9-M058_S+iaa_9 5.326456e+00 -113.5312143 124.184126
## M248_S+lowcyto_9-M058_S+iaa_9 -4.371883e+00 -123.2295530 114.485788
## M248_S+lowga_9-M058_S+iaa_9 2.923335e+02 176.6459595 408.021082
## M248_S+only_9-M058_S+iaa_9 2.463037e+01 -65.1330983 114.393842
## M058_S+lowacc_9-M058_S+lowaba_9 1.110355e+00 -114.5772064 116.797916
## M058_S+lowcyto_9-M058_S+lowaba_9 -3.311814e-01 -116.0187425 115.356380
## M058_S+lowga_9-M058_S+lowaba_9 5.443662e+00 -110.2438989 121.131223
## M058_S+only_9-M058_S+lowaba_9 1.935323e+00 -88.8833967 92.754042
## M248_S+hiaba_9-M058_S+lowaba_9 2.483030e+00 -116.3746402 121.340700
## M248_S+hiacc_9-M058_S+lowaba_9 3.165592e+00 -112.5219690 118.853153
## M248_S+hicyto_9-M058_S+lowaba_9 -3.688622e-01 -123.0740506 122.336326
## M248_S+higa_9-M058_S+lowaba_9 1.351856e+02 19.4980389 250.873161
## M248_S+iaa_9-M058_S+lowaba_9 5.750032e+00 -109.9375289 121.437593
## M248_S+lowaba_9-M058_S+lowaba_9 7.876923e+00 -107.8106376 123.564485
## M248_S+lowacc_9-M058_S+lowaba_9 9.475995e+00 -109.3816749 128.333666
## M248_S+lowcyto_9-M058_S+lowaba_9 -2.223433e-01 -119.0800136 118.635327
## M248_S+lowga_9-M058_S+lowaba_9 2.964831e+02 180.7954989 412.170621
## M248_S+only_9-M058_S+lowaba_9 2.877991e+01 -60.9835589 118.543381
## M058_S+lowcyto_9-M058_S+lowacc_9 -1.441536e+00 -117.1290972 114.246025
## M058_S+lowga_9-M058_S+lowacc_9 4.333308e+00 -111.3542536 120.020869
## M058_S+only_9-M058_S+lowacc_9 8.249682e-01 -89.9937514 91.643688
## M248_S+hiaba_9-M058_S+lowacc_9 1.372675e+00 -117.4849949 120.230346
## M248_S+hiacc_9-M058_S+lowacc_9 2.055237e+00 -113.6323237 117.742798
## M248_S+hicyto_9-M058_S+lowacc_9 -1.479217e+00 -124.1844053 121.225971
## M248_S+higa_9-M058_S+lowacc_9 1.340752e+02 18.3876842 249.762806
## M248_S+iaa_9-M058_S+lowacc_9 4.639677e+00 -111.0478836 120.327239
## M248_S+lowaba_9-M058_S+lowacc_9 6.766569e+00 -108.9209923 122.454130
## M248_S+lowacc_9-M058_S+lowacc_9 8.365641e+00 -110.4920296 127.223311
## M248_S+lowcyto_9-M058_S+lowacc_9 -1.332698e+00 -120.1903683 117.524972
## M248_S+lowga_9-M058_S+lowacc_9 2.953727e+02 179.6851442 411.060266
## M248_S+only_9-M058_S+lowacc_9 2.766956e+01 -62.0939136 117.433027
## M058_S+lowga_9-M058_S+lowcyto_9 5.774844e+00 -109.9127175 121.462405
## M058_S+only_9-M058_S+lowcyto_9 2.266504e+00 -88.5522153 93.085224
## M248_S+hiaba_9-M058_S+lowcyto_9 2.814211e+00 -116.0434588 121.671882
## M248_S+hiacc_9-M058_S+lowcyto_9 3.496773e+00 -112.1907876 119.184335
## M248_S+hicyto_9-M058_S+lowcyto_9 -3.768083e-02 -122.7428692 122.667508
## M248_S+higa_9-M058_S+lowcyto_9 1.355168e+02 19.8292203 251.204342
## M248_S+iaa_9-M058_S+lowcyto_9 6.081214e+00 -109.6063475 121.768775
## M248_S+lowaba_9-M058_S+lowcyto_9 8.208105e+00 -107.4794562 123.895666
## M248_S+lowacc_9-M058_S+lowcyto_9 9.807177e+00 -109.0504935 128.664847
## M248_S+lowcyto_9-M058_S+lowcyto_9 1.088381e-01 -118.7488322 118.966508
## M248_S+lowga_9-M058_S+lowcyto_9 2.968142e+02 181.1266803 412.501802
## M248_S+only_9-M058_S+lowcyto_9 2.911109e+01 -60.6523775 118.874563
## M058_S+only_9-M058_S+lowga_9 -3.508339e+00 -94.3270589 87.310380
## M248_S+hiaba_9-M058_S+lowga_9 -2.960632e+00 -121.8183024 115.897038
## M248_S+hiacc_9-M058_S+lowga_9 -2.278070e+00 -117.9656312 113.409491
## M248_S+hicyto_9-M058_S+lowga_9 -5.812524e+00 -128.5177128 116.892664
## M248_S+higa_9-M058_S+lowga_9 1.297419e+02 14.0543767 245.429499
## M248_S+iaa_9-M058_S+lowga_9 3.063700e-01 -115.3811911 115.993931
## M248_S+lowaba_9-M058_S+lowga_9 2.433261e+00 -113.2542998 118.120822
## M248_S+lowacc_9-M058_S+lowga_9 4.032333e+00 -114.8253371 122.890003
## M248_S+lowcyto_9-M058_S+lowga_9 -5.666006e+00 -124.5236758 113.191665
## M248_S+lowga_9-M058_S+lowga_9 2.910394e+02 175.3518367 406.726959
## M248_S+only_9-M058_S+lowga_9 2.333625e+01 -66.4272211 113.099719
## M248_S+hiaba_9-M058_S+only_9 5.477072e-01 -94.2762023 95.371617
## M248_S+hiacc_9-M058_S+only_9 1.230269e+00 -89.5884503 92.048989
## M248_S+hicyto_9-M058_S+only_9 -2.304185e+00 -101.9083582 97.299988
## M248_S+higa_9-M058_S+only_9 1.332503e+02 42.4315576 224.068997
## M248_S+iaa_9-M058_S+only_9 3.814709e+00 -87.0040102 94.633429
## M248_S+lowaba_9-M058_S+only_9 5.941601e+00 -84.8771189 96.760320
## M248_S+lowacc_9-M058_S+only_9 7.540672e+00 -87.2832370 102.364582
## M248_S+lowcyto_9-M058_S+only_9 -2.157666e+00 -96.9815757 92.666243
## M248_S+lowga_9-M058_S+only_9 2.945477e+02 203.7290176 385.366457
## M248_S+only_9-M058_S+only_9 2.684459e+01 -27.2100932 80.899270
## M248_S+hiacc_9-M248_S+hiaba_9 6.825621e-01 -118.1751082 119.540232
## M248_S+hicyto_9-M248_S+hiaba_9 -2.851892e+00 -128.5503300 122.846546
## M248_S+higa_9-M248_S+hiaba_9 1.327026e+02 13.8448997 251.560240
## M248_S+iaa_9-M248_S+hiaba_9 3.267002e+00 -115.5906681 122.124672
## M248_S+lowaba_9-M248_S+hiaba_9 5.393893e+00 -113.4637768 124.251564
## M248_S+lowacc_9-M248_S+hiaba_9 6.992965e+00 -114.9524313 128.938362
## M248_S+lowcyto_9-M248_S+hiaba_9 -2.705373e+00 -124.6507700 119.240023
## M248_S+lowga_9-M248_S+hiaba_9 2.940000e+02 175.1423597 412.857700
## M248_S+only_9-M248_S+hiaba_9 2.629688e+01 -67.5168414 120.110604
## M248_S+hicyto_9-M248_S+hiacc_9 -3.534454e+00 -126.2396427 119.170734
## M248_S+higa_9-M248_S+hiacc_9 1.320200e+02 16.3324468 247.707569
## M248_S+iaa_9-M248_S+hiacc_9 2.584440e+00 -113.1031210 118.272001
## M248_S+lowaba_9-M248_S+hiacc_9 4.711331e+00 -110.9762297 120.398892
## M248_S+lowacc_9-M248_S+hiacc_9 6.310403e+00 -112.5472670 125.168073
## M248_S+lowcyto_9-M248_S+hiacc_9 -3.387935e+00 -122.2456057 115.469735
## M248_S+lowga_9-M248_S+hiacc_9 2.933175e+02 177.6299068 409.005029
## M248_S+only_9-M248_S+hiacc_9 2.561432e+01 -64.1491510 115.377789
## M248_S+higa_9-M248_S+hicyto_9 1.355545e+02 12.8492738 258.259651
## M248_S+iaa_9-M248_S+hicyto_9 6.118894e+00 -116.5862940 128.824083
## M248_S+lowaba_9-M248_S+hicyto_9 8.245786e+00 -114.4594027 130.950974
## M248_S+lowacc_9-M248_S+hicyto_9 9.844858e+00 -115.8535802 135.543295
## M248_S+lowcyto_9-M248_S+hicyto_9 1.465189e-01 -125.5519188 125.844957
## M248_S+lowga_9-M248_S+hicyto_9 2.968519e+02 174.1467338 419.557111
## M248_S+only_9-M248_S+hicyto_9 2.914877e+01 -69.4941789 127.791726
## M248_S+iaa_9-M248_S+higa_9 -1.294356e+02 -245.1231289 -13.748007
## M248_S+lowaba_9-M248_S+higa_9 -1.273087e+02 -242.9962376 -11.621115
## M248_S+lowacc_9-M248_S+higa_9 -1.257096e+02 -244.5672749 -6.851934
## M248_S+lowcyto_9-M248_S+higa_9 -1.354079e+02 -254.2656136 -16.550273
## M248_S+lowga_9-M248_S+higa_9 1.612975e+02 45.6098989 276.985021
## M248_S+only_9-M248_S+higa_9 -1.064057e+02 -196.1691589 -16.642219
## M248_S+lowaba_9-M248_S+iaa_9 2.126891e+00 -113.5606698 117.814452
## M248_S+lowacc_9-M248_S+iaa_9 3.725963e+00 -115.1317071 122.583633
## M248_S+lowcyto_9-M248_S+iaa_9 -5.972376e+00 -124.8300458 112.885295
## M248_S+lowga_9-M248_S+iaa_9 2.907330e+02 175.0454667 406.420589
## M248_S+only_9-M248_S+iaa_9 2.302988e+01 -66.7335911 112.793349
## M248_S+lowacc_9-M248_S+lowaba_9 1.599072e+00 -117.2585984 120.456742
## M248_S+lowcyto_9-M248_S+lowaba_9 -8.099267e+00 -126.9569371 110.758403
## M248_S+lowga_9-M248_S+lowaba_9 2.886061e+02 172.9185754 404.293698
## M248_S+only_9-M248_S+lowaba_9 2.090299e+01 -68.8604824 110.666458
## M248_S+lowcyto_9-M248_S+lowacc_9 -9.698339e+00 -131.6437353 112.247058
## M248_S+lowga_9-M248_S+lowacc_9 2.870071e+02 168.1493944 405.864735
## M248_S+only_9-M248_S+lowacc_9 1.930392e+01 -74.5098068 113.117638
## M248_S+lowga_9-M248_S+lowcyto_9 2.967054e+02 177.8477331 415.563074
## M248_S+only_9-M248_S+lowcyto_9 2.900225e+01 -64.8114681 122.815977
## M248_S+only_9-M248_S+lowga_9 -2.677031e+02 -357.4666189 -177.939679
## p adj
## LA1511_S+hiacc_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+hicyto_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+higa_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+iaa_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+only_9-LA1511_S+hiaba_9 1.0000000
## M058_S+hiaba_9-LA1511_S+hiaba_9 1.0000000
## M058_S+hiacc_9-LA1511_S+hiaba_9 1.0000000
## M058_S+hicyto_9-LA1511_S+hiaba_9 1.0000000
## M058_S+higa_9-LA1511_S+hiaba_9 1.0000000
## M058_S+iaa_9-LA1511_S+hiaba_9 1.0000000
## M058_S+lowaba_9-LA1511_S+hiaba_9 1.0000000
## M058_S+lowacc_9-LA1511_S+hiaba_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+hiaba_9 1.0000000
## M058_S+lowga_9-LA1511_S+hiaba_9 1.0000000
## M058_S+only_9-LA1511_S+hiaba_9 1.0000000
## M248_S+hiaba_9-LA1511_S+hiaba_9 1.0000000
## M248_S+hiacc_9-LA1511_S+hiaba_9 1.0000000
## M248_S+hicyto_9-LA1511_S+hiaba_9 1.0000000
## M248_S+higa_9-LA1511_S+hiaba_9 0.0414876
## M248_S+iaa_9-LA1511_S+hiaba_9 1.0000000
## M248_S+lowaba_9-LA1511_S+hiaba_9 1.0000000
## M248_S+lowacc_9-LA1511_S+hiaba_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+hiaba_9 1.0000000
## M248_S+lowga_9-LA1511_S+hiaba_9 0.0000000
## M248_S+only_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+hicyto_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+higa_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+iaa_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+only_9-LA1511_S+hiacc_9 1.0000000
## M058_S+hiaba_9-LA1511_S+hiacc_9 1.0000000
## M058_S+hiacc_9-LA1511_S+hiacc_9 1.0000000
## M058_S+hicyto_9-LA1511_S+hiacc_9 1.0000000
## M058_S+higa_9-LA1511_S+hiacc_9 1.0000000
## M058_S+iaa_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowaba_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowacc_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowga_9-LA1511_S+hiacc_9 1.0000000
## M058_S+only_9-LA1511_S+hiacc_9 1.0000000
## M248_S+hiaba_9-LA1511_S+hiacc_9 1.0000000
## M248_S+hiacc_9-LA1511_S+hiacc_9 1.0000000
## M248_S+hicyto_9-LA1511_S+hiacc_9 1.0000000
## M248_S+higa_9-LA1511_S+hiacc_9 0.0468696
## M248_S+iaa_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowaba_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowacc_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowga_9-LA1511_S+hiacc_9 0.0000000
## M248_S+only_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+higa_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+iaa_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+only_9-LA1511_S+hicyto_9 1.0000000
## M058_S+hiaba_9-LA1511_S+hicyto_9 1.0000000
## M058_S+hiacc_9-LA1511_S+hicyto_9 1.0000000
## M058_S+hicyto_9-LA1511_S+hicyto_9 1.0000000
## M058_S+higa_9-LA1511_S+hicyto_9 1.0000000
## M058_S+iaa_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowaba_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowacc_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowga_9-LA1511_S+hicyto_9 1.0000000
## M058_S+only_9-LA1511_S+hicyto_9 1.0000000
## M248_S+hiaba_9-LA1511_S+hicyto_9 1.0000000
## M248_S+hiacc_9-LA1511_S+hicyto_9 1.0000000
## M248_S+hicyto_9-LA1511_S+hicyto_9 1.0000000
## M248_S+higa_9-LA1511_S+hicyto_9 0.0072125
## M248_S+iaa_9-LA1511_S+hicyto_9 1.0000000
## M248_S+lowaba_9-LA1511_S+hicyto_9 1.0000000
## M248_S+lowacc_9-LA1511_S+hicyto_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+hicyto_9 1.0000000
## M248_S+lowga_9-LA1511_S+hicyto_9 0.0000000
## M248_S+only_9-LA1511_S+hicyto_9 0.9999984
## LA1511_S+iaa_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+higa_9 1.0000000
## LA1511_S+only_9-LA1511_S+higa_9 1.0000000
## M058_S+hiaba_9-LA1511_S+higa_9 1.0000000
## M058_S+hiacc_9-LA1511_S+higa_9 1.0000000
## M058_S+hicyto_9-LA1511_S+higa_9 1.0000000
## M058_S+higa_9-LA1511_S+higa_9 1.0000000
## M058_S+iaa_9-LA1511_S+higa_9 1.0000000
## M058_S+lowaba_9-LA1511_S+higa_9 1.0000000
## M058_S+lowacc_9-LA1511_S+higa_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+higa_9 1.0000000
## M058_S+lowga_9-LA1511_S+higa_9 1.0000000
## M058_S+only_9-LA1511_S+higa_9 1.0000000
## M248_S+hiaba_9-LA1511_S+higa_9 1.0000000
## M248_S+hiacc_9-LA1511_S+higa_9 1.0000000
## M248_S+hicyto_9-LA1511_S+higa_9 1.0000000
## M248_S+higa_9-LA1511_S+higa_9 0.0259126
## M248_S+iaa_9-LA1511_S+higa_9 1.0000000
## M248_S+lowaba_9-LA1511_S+higa_9 1.0000000
## M248_S+lowacc_9-LA1511_S+higa_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+higa_9 1.0000000
## M248_S+lowga_9-LA1511_S+higa_9 0.0000000
## M248_S+only_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+only_9-LA1511_S+iaa_9 1.0000000
## M058_S+hiaba_9-LA1511_S+iaa_9 1.0000000
## M058_S+hiacc_9-LA1511_S+iaa_9 1.0000000
## M058_S+hicyto_9-LA1511_S+iaa_9 1.0000000
## M058_S+higa_9-LA1511_S+iaa_9 1.0000000
## M058_S+iaa_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowaba_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowacc_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowga_9-LA1511_S+iaa_9 1.0000000
## M058_S+only_9-LA1511_S+iaa_9 1.0000000
## M248_S+hiaba_9-LA1511_S+iaa_9 1.0000000
## M248_S+hiacc_9-LA1511_S+iaa_9 1.0000000
## M248_S+hicyto_9-LA1511_S+iaa_9 1.0000000
## M248_S+higa_9-LA1511_S+iaa_9 0.0123029
## M248_S+iaa_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowaba_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowacc_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowga_9-LA1511_S+iaa_9 0.0000000
## M248_S+only_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+lowaba_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+lowaba_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+lowaba_9 1.0000000
## LA1511_S+only_9-LA1511_S+lowaba_9 1.0000000
## M058_S+hiaba_9-LA1511_S+lowaba_9 1.0000000
## M058_S+hiacc_9-LA1511_S+lowaba_9 1.0000000
## M058_S+hicyto_9-LA1511_S+lowaba_9 1.0000000
## M058_S+higa_9-LA1511_S+lowaba_9 1.0000000
## M058_S+iaa_9-LA1511_S+lowaba_9 1.0000000
## M058_S+lowaba_9-LA1511_S+lowaba_9 1.0000000
## M058_S+lowacc_9-LA1511_S+lowaba_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+lowaba_9 1.0000000
## M058_S+lowga_9-LA1511_S+lowaba_9 1.0000000
## M058_S+only_9-LA1511_S+lowaba_9 1.0000000
## M248_S+hiaba_9-LA1511_S+lowaba_9 1.0000000
## M248_S+hiacc_9-LA1511_S+lowaba_9 1.0000000
## M248_S+hicyto_9-LA1511_S+lowaba_9 1.0000000
## M248_S+higa_9-LA1511_S+lowaba_9 0.0046720
## M248_S+iaa_9-LA1511_S+lowaba_9 1.0000000
## M248_S+lowaba_9-LA1511_S+lowaba_9 1.0000000
## M248_S+lowacc_9-LA1511_S+lowaba_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+lowaba_9 1.0000000
## M248_S+lowga_9-LA1511_S+lowaba_9 0.0000000
## M248_S+only_9-LA1511_S+lowaba_9 0.9999966
## LA1511_S+lowcyto_9-LA1511_S+lowacc_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+lowacc_9 1.0000000
## LA1511_S+only_9-LA1511_S+lowacc_9 1.0000000
## M058_S+hiaba_9-LA1511_S+lowacc_9 1.0000000
## M058_S+hiacc_9-LA1511_S+lowacc_9 1.0000000
## M058_S+hicyto_9-LA1511_S+lowacc_9 1.0000000
## M058_S+higa_9-LA1511_S+lowacc_9 1.0000000
## M058_S+iaa_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowaba_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowacc_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowga_9-LA1511_S+lowacc_9 1.0000000
## M058_S+only_9-LA1511_S+lowacc_9 1.0000000
## M248_S+hiaba_9-LA1511_S+lowacc_9 1.0000000
## M248_S+hiacc_9-LA1511_S+lowacc_9 1.0000000
## M248_S+hicyto_9-LA1511_S+lowacc_9 1.0000000
## M248_S+higa_9-LA1511_S+lowacc_9 0.0416779
## M248_S+iaa_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowaba_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowacc_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowga_9-LA1511_S+lowacc_9 0.0000000
## M248_S+only_9-LA1511_S+lowacc_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+lowcyto_9 1.0000000
## LA1511_S+only_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+hiaba_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+hiacc_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+hicyto_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+higa_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+iaa_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowaba_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowacc_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowga_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+only_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+hiaba_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+hiacc_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+hicyto_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+higa_9-LA1511_S+lowcyto_9 0.0072362
## M248_S+iaa_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowaba_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowacc_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowga_9-LA1511_S+lowcyto_9 0.0000000
## M248_S+only_9-LA1511_S+lowcyto_9 0.9999984
## LA1511_S+only_9-LA1511_S+lowga_9 1.0000000
## M058_S+hiaba_9-LA1511_S+lowga_9 1.0000000
## M058_S+hiacc_9-LA1511_S+lowga_9 1.0000000
## M058_S+hicyto_9-LA1511_S+lowga_9 1.0000000
## M058_S+higa_9-LA1511_S+lowga_9 1.0000000
## M058_S+iaa_9-LA1511_S+lowga_9 1.0000000
## M058_S+lowaba_9-LA1511_S+lowga_9 1.0000000
## M058_S+lowacc_9-LA1511_S+lowga_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+lowga_9 1.0000000
## M058_S+lowga_9-LA1511_S+lowga_9 1.0000000
## M058_S+only_9-LA1511_S+lowga_9 1.0000000
## M248_S+hiaba_9-LA1511_S+lowga_9 1.0000000
## M248_S+hiacc_9-LA1511_S+lowga_9 1.0000000
## M248_S+hicyto_9-LA1511_S+lowga_9 1.0000000
## M248_S+higa_9-LA1511_S+lowga_9 0.0035132
## M248_S+iaa_9-LA1511_S+lowga_9 1.0000000
## M248_S+lowaba_9-LA1511_S+lowga_9 1.0000000
## M248_S+lowacc_9-LA1511_S+lowga_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+lowga_9 1.0000000
## M248_S+lowga_9-LA1511_S+lowga_9 0.0000000
## M248_S+only_9-LA1511_S+lowga_9 0.9999965
## M058_S+hiaba_9-LA1511_S+only_9 1.0000000
## M058_S+hiacc_9-LA1511_S+only_9 1.0000000
## M058_S+hicyto_9-LA1511_S+only_9 1.0000000
## M058_S+higa_9-LA1511_S+only_9 1.0000000
## M058_S+iaa_9-LA1511_S+only_9 1.0000000
## M058_S+lowaba_9-LA1511_S+only_9 1.0000000
## M058_S+lowacc_9-LA1511_S+only_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+only_9 1.0000000
## M058_S+lowga_9-LA1511_S+only_9 1.0000000
## M058_S+only_9-LA1511_S+only_9 1.0000000
## M248_S+hiaba_9-LA1511_S+only_9 1.0000000
## M248_S+hiacc_9-LA1511_S+only_9 1.0000000
## M248_S+hicyto_9-LA1511_S+only_9 1.0000000
## M248_S+higa_9-LA1511_S+only_9 0.0000649
## M248_S+iaa_9-LA1511_S+only_9 1.0000000
## M248_S+lowaba_9-LA1511_S+only_9 1.0000000
## M248_S+lowacc_9-LA1511_S+only_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+only_9 1.0000000
## M248_S+lowga_9-LA1511_S+only_9 0.0000000
## M248_S+only_9-LA1511_S+only_9 0.9995661
## M058_S+hiacc_9-M058_S+hiaba_9 1.0000000
## M058_S+hicyto_9-M058_S+hiaba_9 1.0000000
## M058_S+higa_9-M058_S+hiaba_9 1.0000000
## M058_S+iaa_9-M058_S+hiaba_9 1.0000000
## M058_S+lowaba_9-M058_S+hiaba_9 1.0000000
## M058_S+lowacc_9-M058_S+hiaba_9 1.0000000
## M058_S+lowcyto_9-M058_S+hiaba_9 1.0000000
## M058_S+lowga_9-M058_S+hiaba_9 1.0000000
## M058_S+only_9-M058_S+hiaba_9 1.0000000
## M248_S+hiaba_9-M058_S+hiaba_9 1.0000000
## M248_S+hiacc_9-M058_S+hiaba_9 1.0000000
## M248_S+hicyto_9-M058_S+hiaba_9 1.0000000
## M248_S+higa_9-M058_S+hiaba_9 0.0127351
## M248_S+iaa_9-M058_S+hiaba_9 1.0000000
## M248_S+lowaba_9-M058_S+hiaba_9 1.0000000
## M248_S+lowacc_9-M058_S+hiaba_9 1.0000000
## M248_S+lowcyto_9-M058_S+hiaba_9 1.0000000
## M248_S+lowga_9-M058_S+hiaba_9 0.0000000
## M248_S+only_9-M058_S+hiaba_9 0.9999996
## M058_S+hicyto_9-M058_S+hiacc_9 1.0000000
## M058_S+higa_9-M058_S+hiacc_9 1.0000000
## M058_S+iaa_9-M058_S+hiacc_9 1.0000000
## M058_S+lowaba_9-M058_S+hiacc_9 1.0000000
## M058_S+lowacc_9-M058_S+hiacc_9 1.0000000
## M058_S+lowcyto_9-M058_S+hiacc_9 1.0000000
## M058_S+lowga_9-M058_S+hiacc_9 1.0000000
## M058_S+only_9-M058_S+hiacc_9 1.0000000
## M248_S+hiaba_9-M058_S+hiacc_9 1.0000000
## M248_S+hiacc_9-M058_S+hiacc_9 1.0000000
## M248_S+hicyto_9-M058_S+hiacc_9 1.0000000
## M248_S+higa_9-M058_S+hiacc_9 0.0048181
## M248_S+iaa_9-M058_S+hiacc_9 1.0000000
## M248_S+lowaba_9-M058_S+hiacc_9 1.0000000
## M248_S+lowacc_9-M058_S+hiacc_9 1.0000000
## M248_S+lowcyto_9-M058_S+hiacc_9 1.0000000
## M248_S+lowga_9-M058_S+hiacc_9 0.0000000
## M248_S+only_9-M058_S+hiacc_9 0.9999972
## M058_S+higa_9-M058_S+hicyto_9 1.0000000
## M058_S+iaa_9-M058_S+hicyto_9 1.0000000
## M058_S+lowaba_9-M058_S+hicyto_9 1.0000000
## M058_S+lowacc_9-M058_S+hicyto_9 1.0000000
## M058_S+lowcyto_9-M058_S+hicyto_9 1.0000000
## M058_S+lowga_9-M058_S+hicyto_9 1.0000000
## M058_S+only_9-M058_S+hicyto_9 1.0000000
## M248_S+hiaba_9-M058_S+hicyto_9 1.0000000
## M248_S+hiacc_9-M058_S+hicyto_9 1.0000000
## M248_S+hicyto_9-M058_S+hicyto_9 1.0000000
## M248_S+higa_9-M058_S+hicyto_9 0.0122522
## M248_S+iaa_9-M058_S+hicyto_9 1.0000000
## M248_S+lowaba_9-M058_S+hicyto_9 1.0000000
## M248_S+lowacc_9-M058_S+hicyto_9 1.0000000
## M248_S+lowcyto_9-M058_S+hicyto_9 1.0000000
## M248_S+lowga_9-M058_S+hicyto_9 0.0000000
## M248_S+only_9-M058_S+hicyto_9 0.9999995
## M058_S+iaa_9-M058_S+higa_9 1.0000000
## M058_S+lowaba_9-M058_S+higa_9 1.0000000
## M058_S+lowacc_9-M058_S+higa_9 1.0000000
## M058_S+lowcyto_9-M058_S+higa_9 1.0000000
## M058_S+lowga_9-M058_S+higa_9 1.0000000
## M058_S+only_9-M058_S+higa_9 1.0000000
## M248_S+hiaba_9-M058_S+higa_9 1.0000000
## M248_S+hiacc_9-M058_S+higa_9 1.0000000
## M248_S+hicyto_9-M058_S+higa_9 1.0000000
## M248_S+higa_9-M058_S+higa_9 0.0063161
## M248_S+iaa_9-M058_S+higa_9 1.0000000
## M248_S+lowaba_9-M058_S+higa_9 1.0000000
## M248_S+lowacc_9-M058_S+higa_9 1.0000000
## M248_S+lowcyto_9-M058_S+higa_9 1.0000000
## M248_S+lowga_9-M058_S+higa_9 0.0000000
## M248_S+only_9-M058_S+higa_9 0.9999995
## M058_S+lowaba_9-M058_S+iaa_9 1.0000000
## M058_S+lowacc_9-M058_S+iaa_9 1.0000000
## M058_S+lowcyto_9-M058_S+iaa_9 1.0000000
## M058_S+lowga_9-M058_S+iaa_9 1.0000000
## M058_S+only_9-M058_S+iaa_9 1.0000000
## M248_S+hiaba_9-M058_S+iaa_9 1.0000000
## M248_S+hiacc_9-M058_S+iaa_9 1.0000000
## M248_S+hicyto_9-M058_S+iaa_9 1.0000000
## M248_S+higa_9-M058_S+iaa_9 0.0081137
## M248_S+iaa_9-M058_S+iaa_9 1.0000000
## M248_S+lowaba_9-M058_S+iaa_9 1.0000000
## M248_S+lowacc_9-M058_S+iaa_9 1.0000000
## M248_S+lowcyto_9-M058_S+iaa_9 1.0000000
## M248_S+lowga_9-M058_S+iaa_9 0.0000000
## M248_S+only_9-M058_S+iaa_9 0.9999999
## M058_S+lowacc_9-M058_S+lowaba_9 1.0000000
## M058_S+lowcyto_9-M058_S+lowaba_9 1.0000000
## M058_S+lowga_9-M058_S+lowaba_9 1.0000000
## M058_S+only_9-M058_S+lowaba_9 1.0000000
## M248_S+hiaba_9-M058_S+lowaba_9 1.0000000
## M248_S+hiacc_9-M058_S+lowaba_9 1.0000000
## M248_S+hicyto_9-M058_S+lowaba_9 1.0000000
## M248_S+higa_9-M058_S+lowaba_9 0.0047001
## M248_S+iaa_9-M058_S+lowaba_9 1.0000000
## M248_S+lowaba_9-M058_S+lowaba_9 1.0000000
## M248_S+lowacc_9-M058_S+lowaba_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowaba_9 1.0000000
## M248_S+lowga_9-M058_S+lowaba_9 0.0000000
## M248_S+only_9-M058_S+lowaba_9 0.9999968
## M058_S+lowcyto_9-M058_S+lowacc_9 1.0000000
## M058_S+lowga_9-M058_S+lowacc_9 1.0000000
## M058_S+only_9-M058_S+lowacc_9 1.0000000
## M248_S+hiaba_9-M058_S+lowacc_9 1.0000000
## M248_S+hiacc_9-M058_S+lowacc_9 1.0000000
## M248_S+hicyto_9-M058_S+lowacc_9 1.0000000
## M248_S+higa_9-M058_S+lowacc_9 0.0054509
## M248_S+iaa_9-M058_S+lowacc_9 1.0000000
## M248_S+lowaba_9-M058_S+lowacc_9 1.0000000
## M248_S+lowacc_9-M058_S+lowacc_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowacc_9 1.0000000
## M248_S+lowga_9-M058_S+lowacc_9 0.0000000
## M248_S+only_9-M058_S+lowacc_9 0.9999986
## M058_S+lowga_9-M058_S+lowcyto_9 1.0000000
## M058_S+only_9-M058_S+lowcyto_9 1.0000000
## M248_S+hiaba_9-M058_S+lowcyto_9 1.0000000
## M248_S+hiacc_9-M058_S+lowcyto_9 1.0000000
## M248_S+hicyto_9-M058_S+lowcyto_9 1.0000000
## M248_S+higa_9-M058_S+lowcyto_9 0.0044956
## M248_S+iaa_9-M058_S+lowcyto_9 1.0000000
## M248_S+lowaba_9-M058_S+lowcyto_9 1.0000000
## M248_S+lowacc_9-M058_S+lowcyto_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowcyto_9 1.0000000
## M248_S+lowga_9-M058_S+lowcyto_9 0.0000000
## M248_S+only_9-M058_S+lowcyto_9 0.9999958
## M058_S+only_9-M058_S+lowga_9 1.0000000
## M248_S+hiaba_9-M058_S+lowga_9 1.0000000
## M248_S+hiacc_9-M058_S+lowga_9 1.0000000
## M248_S+hicyto_9-M058_S+lowga_9 1.0000000
## M248_S+higa_9-M058_S+lowga_9 0.0095771
## M248_S+iaa_9-M058_S+lowga_9 1.0000000
## M248_S+lowaba_9-M058_S+lowga_9 1.0000000
## M248_S+lowacc_9-M058_S+lowga_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowga_9 1.0000000
## M248_S+lowga_9-M058_S+lowga_9 0.0000000
## M248_S+only_9-M058_S+lowga_9 1.0000000
## M248_S+hiaba_9-M058_S+only_9 1.0000000
## M248_S+hiacc_9-M058_S+only_9 1.0000000
## M248_S+hicyto_9-M058_S+only_9 1.0000000
## M248_S+higa_9-M058_S+only_9 0.0000239
## M248_S+iaa_9-M058_S+only_9 1.0000000
## M248_S+lowaba_9-M058_S+only_9 1.0000000
## M248_S+lowacc_9-M058_S+only_9 1.0000000
## M248_S+lowcyto_9-M058_S+only_9 1.0000000
## M248_S+lowga_9-M058_S+only_9 0.0000000
## M248_S+only_9-M058_S+only_9 0.9902813
## M248_S+hiacc_9-M248_S+hiaba_9 1.0000000
## M248_S+hicyto_9-M248_S+hiaba_9 1.0000000
## M248_S+higa_9-M248_S+hiaba_9 0.0103071
## M248_S+iaa_9-M248_S+hiaba_9 1.0000000
## M248_S+lowaba_9-M248_S+hiaba_9 1.0000000
## M248_S+lowacc_9-M248_S+hiaba_9 1.0000000
## M248_S+lowcyto_9-M248_S+hiaba_9 1.0000000
## M248_S+lowga_9-M248_S+hiaba_9 0.0000000
## M248_S+only_9-M248_S+hiaba_9 0.9999998
## M248_S+hicyto_9-M248_S+hiacc_9 1.0000000
## M248_S+higa_9-M248_S+hiacc_9 0.0071424
## M248_S+iaa_9-M248_S+hiacc_9 1.0000000
## M248_S+lowaba_9-M248_S+hiacc_9 1.0000000
## M248_S+lowacc_9-M248_S+hiacc_9 1.0000000
## M248_S+lowcyto_9-M248_S+hiacc_9 1.0000000
## M248_S+lowga_9-M248_S+hiacc_9 0.0000000
## M248_S+only_9-M248_S+hiacc_9 0.9999998
## M248_S+higa_9-M248_S+hicyto_9 0.0122298
## M248_S+iaa_9-M248_S+hicyto_9 1.0000000
## M248_S+lowaba_9-M248_S+hicyto_9 1.0000000
## M248_S+lowacc_9-M248_S+hicyto_9 1.0000000
## M248_S+lowcyto_9-M248_S+hicyto_9 1.0000000
## M248_S+lowga_9-M248_S+hicyto_9 0.0000000
## M248_S+only_9-M248_S+hicyto_9 0.9999995
## M248_S+iaa_9-M248_S+higa_9 0.0099574
## M248_S+lowaba_9-M248_S+higa_9 0.0130039
## M248_S+lowacc_9-M248_S+higa_9 0.0236406
## M248_S+lowcyto_9-M248_S+higa_9 0.0073531
## M248_S+lowga_9-M248_S+higa_9 0.0000969
## M248_S+only_9-M248_S+higa_9 0.0036098
## M248_S+lowaba_9-M248_S+iaa_9 1.0000000
## M248_S+lowacc_9-M248_S+iaa_9 1.0000000
## M248_S+lowcyto_9-M248_S+iaa_9 1.0000000
## M248_S+lowga_9-M248_S+iaa_9 0.0000000
## M248_S+only_9-M248_S+iaa_9 1.0000000
## M248_S+lowacc_9-M248_S+lowaba_9 1.0000000
## M248_S+lowcyto_9-M248_S+lowaba_9 1.0000000
## M248_S+lowga_9-M248_S+lowaba_9 0.0000000
## M248_S+only_9-M248_S+lowaba_9 1.0000000
## M248_S+lowcyto_9-M248_S+lowacc_9 1.0000000
## M248_S+lowga_9-M248_S+lowacc_9 0.0000000
## M248_S+only_9-M248_S+lowacc_9 1.0000000
## M248_S+lowga_9-M248_S+lowcyto_9 0.0000000
## M248_S+only_9-M248_S+lowcyto_9 0.9999985
## M248_S+only_9-M248_S+lowga_9 0.0000000P7 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P7)
stat.test## LA1511_S+hiacc_9 LA1511_S+hicyto_9 LA1511_S+higa_9 LA1511_S+iaa_9
## "a" "a" "a" "a"
## LA1511_S+lowaba_9 LA1511_S+lowacc_9 LA1511_S+lowcyto_9 LA1511_S+lowga_9
## "a" "a" "a" "a"
## LA1511_S+only_9 M058_S+hiaba_9 M058_S+hiacc_9 M058_S+hicyto_9
## "a" "a" "a" "a"
## M058_S+higa_9 M058_S+iaa_9 M058_S+lowaba_9 M058_S+lowacc_9
## "a" "a" "a" "a"
## M058_S+lowcyto_9 M058_S+lowga_9 M058_S+only_9 M248_S+hiaba_9
## "a" "a" "a" "a"
## M248_S+hiacc_9 M248_S+hicyto_9 M248_S+higa_9 M248_S+iaa_9
## "a" "a" "b" "a"
## M248_S+lowaba_9 M248_S+lowacc_9 M248_S+lowcyto_9 M248_S+lowga_9
## "a" "a" "a" "c"
## M248_S+only_9 LA1511_S+hiaba_9
## "a" "a"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "S+hiacc"test$info[[1]][3]## [1] "9"test$Accession <- "none"
test$All.condition<- "none"
test$Day<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
test$Day[i] <- test$info[[i]][3]
}
test2 <- test[,c(5:7,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
all_data2all_data2$All.condition <- factor(all_data2$All.condition, levels = c("S+only", "S+iaa", "S+lowacc", "S+hiacc", "S+lowaba", "S+hiaba", "S+lowga", "S+higa", "S+lowcyto", "S+hicyto"))
all_data3 <- subset(all_data2, all_data2$Distance.squared < 175)
distance_all <- ggplot(data = all_data3, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_all <- distance_all + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_all <- distance_all + facet_grid(~ Accession, scales = "free_y")
distance_all <- distance_all + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_all <- distance_all + scale_color_manual(values = c("blueviolet","cyan", "pink", "pink4", "green","green4", "magenta", "magenta4", "red1", "red4"))
distance_all <- distance_all + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 200)
distance_all <- distance_all + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_all <- distance_all + rremove("legend")
distance_all
aov(Alpha ~ All.ID2, data = all_data2)## Call:
## aov(formula = Alpha ~ All.ID2, data = all_data2)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 7.362517 21.866992
## Deg. of Freedom 29 353
##
## Residual standard error: 0.2488898
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Alpha ~ All.ID2, data = all_data2))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Alpha ~ All.ID2, data = all_data2)
##
## $All.ID2
## diff lwr upr
## LA1511_S+hiacc_9-LA1511_S+hiaba_9 2.100000e-01 -0.3332237245 0.753223724
## LA1511_S+hicyto_9-LA1511_S+hiaba_9 3.605556e-01 -0.1353375905 0.856448702
## LA1511_S+higa_9-LA1511_S+hiaba_9 1.107576e-01 -0.3667627357 0.588277887
## LA1511_S+iaa_9-LA1511_S+hiaba_9 2.827778e-01 -0.2131153683 0.778670924
## LA1511_S+lowaba_9-LA1511_S+hiaba_9 8.066667e-02 -0.4052074033 0.566540737
## LA1511_S+lowacc_9-LA1511_S+hiaba_9 2.933333e-01 -0.2498903911 0.836557058
## LA1511_S+lowcyto_9-LA1511_S+hiaba_9 3.027778e-01 -0.1931153683 0.798670924
## LA1511_S+lowga_9-LA1511_S+hiaba_9 2.257576e-02 -0.4549445538 0.500096069
## LA1511_S+only_9-LA1511_S+hiaba_9 7.794574e-02 -0.3320955083 0.487986981
## M058_S+hiaba_9-LA1511_S+hiaba_9 -3.208333e-02 -0.5402225987 0.476055932
## M058_S+hiacc_9-LA1511_S+hiaba_9 1.846667e-01 -0.3012074033 0.670540737
## M058_S+hicyto_9-LA1511_S+hiaba_9 1.991667e-01 -0.3089725987 0.707305932
## M058_S+higa_9-LA1511_S+hiaba_9 -1.203333e-01 -0.6062074033 0.365540737
## M058_S+iaa_9-LA1511_S+hiaba_9 1.536667e-01 -0.3322074033 0.639540737
## M058_S+lowaba_9-LA1511_S+hiaba_9 2.996667e-01 -0.1862074033 0.785540737
## M058_S+lowacc_9-LA1511_S+hiaba_9 2.616667e-01 -0.2242074033 0.747540737
## M058_S+lowcyto_9-LA1511_S+hiaba_9 3.176667e-01 -0.1682074033 0.803540737
## M058_S+lowga_9-LA1511_S+hiaba_9 -4.333333e-02 -0.5292074033 0.442540737
## M058_S+only_9-LA1511_S+hiaba_9 3.282946e-02 -0.3772117874 0.442870702
## M248_S+hiaba_9-LA1511_S+hiaba_9 -1.294444e-01 -0.6253375905 0.366448702
## M248_S+hiacc_9-LA1511_S+hiaba_9 2.746667e-01 -0.2112074033 0.760540737
## M248_S+hicyto_9-LA1511_S+hiaba_9 3.866667e-01 -0.1214725987 0.894805932
## M248_S+higa_9-LA1511_S+hiaba_9 1.206667e-01 -0.3652074033 0.606540737
## M248_S+iaa_9-LA1511_S+hiaba_9 2.166667e-01 -0.2692074033 0.702540737
## M248_S+lowaba_9-LA1511_S+hiaba_9 -1.603333e-01 -0.6462074033 0.325540737
## M248_S+lowacc_9-LA1511_S+hiaba_9 2.616667e-01 -0.2342264794 0.757559813
## M248_S+lowcyto_9-LA1511_S+hiaba_9 2.005556e-01 -0.2953375905 0.696448702
## M248_S+lowga_9-LA1511_S+hiaba_9 -1.263333e-01 -0.6122074033 0.359540737
## M248_S+only_9-LA1511_S+hiaba_9 3.207483e-02 -0.3748807763 0.439030436
## LA1511_S+hicyto_9-LA1511_S+hiacc_9 1.505556e-01 -0.3453375905 0.646448702
## LA1511_S+higa_9-LA1511_S+hiacc_9 -9.924242e-02 -0.5767627357 0.378277887
## LA1511_S+iaa_9-LA1511_S+hiacc_9 7.277778e-02 -0.4231153683 0.568670924
## LA1511_S+lowaba_9-LA1511_S+hiacc_9 -1.293333e-01 -0.6152074033 0.356540737
## LA1511_S+lowacc_9-LA1511_S+hiacc_9 8.333333e-02 -0.4598903911 0.626557058
## LA1511_S+lowcyto_9-LA1511_S+hiacc_9 9.277778e-02 -0.4031153683 0.588670924
## LA1511_S+lowga_9-LA1511_S+hiacc_9 -1.874242e-01 -0.6649445538 0.290096069
## LA1511_S+only_9-LA1511_S+hiacc_9 -1.320543e-01 -0.5420955083 0.277986981
## M058_S+hiaba_9-LA1511_S+hiacc_9 -2.420833e-01 -0.7502225987 0.266055932
## M058_S+hiacc_9-LA1511_S+hiacc_9 -2.533333e-02 -0.5112074033 0.460540737
## M058_S+hicyto_9-LA1511_S+hiacc_9 -1.083333e-02 -0.5189725987 0.497305932
## M058_S+higa_9-LA1511_S+hiacc_9 -3.303333e-01 -0.8162074033 0.155540737
## M058_S+iaa_9-LA1511_S+hiacc_9 -5.633333e-02 -0.5422074033 0.429540737
## M058_S+lowaba_9-LA1511_S+hiacc_9 8.966667e-02 -0.3962074033 0.575540737
## M058_S+lowacc_9-LA1511_S+hiacc_9 5.166667e-02 -0.4342074033 0.537540737
## M058_S+lowcyto_9-LA1511_S+hiacc_9 1.076667e-01 -0.3782074033 0.593540737
## M058_S+lowga_9-LA1511_S+hiacc_9 -2.533333e-01 -0.7392074033 0.232540737
## M058_S+only_9-LA1511_S+hiacc_9 -1.771705e-01 -0.5872117874 0.232870702
## M248_S+hiaba_9-LA1511_S+hiacc_9 -3.394444e-01 -0.8353375905 0.156448702
## M248_S+hiacc_9-LA1511_S+hiacc_9 6.466667e-02 -0.4212074033 0.550540737
## M248_S+hicyto_9-LA1511_S+hiacc_9 1.766667e-01 -0.3314725987 0.684805932
## M248_S+higa_9-LA1511_S+hiacc_9 -8.933333e-02 -0.5752074033 0.396540737
## M248_S+iaa_9-LA1511_S+hiacc_9 6.666667e-03 -0.4792074033 0.492540737
## M248_S+lowaba_9-LA1511_S+hiacc_9 -3.703333e-01 -0.8562074033 0.115540737
## M248_S+lowacc_9-LA1511_S+hiacc_9 5.166667e-02 -0.4442264794 0.547559813
## M248_S+lowcyto_9-LA1511_S+hiacc_9 -9.444444e-03 -0.5053375905 0.486448702
## M248_S+lowga_9-LA1511_S+hiacc_9 -3.363333e-01 -0.8222074033 0.149540737
## M248_S+only_9-LA1511_S+hiacc_9 -1.779252e-01 -0.5848807763 0.229030436
## LA1511_S+higa_9-LA1511_S+hicyto_9 -2.497980e-01 -0.6726970757 0.173101116
## LA1511_S+iaa_9-LA1511_S+hicyto_9 -7.777778e-02 -0.5213180915 0.365762536
## LA1511_S+lowaba_9-LA1511_S+hicyto_9 -2.798889e-01 -0.7121985110 0.152420733
## LA1511_S+lowacc_9-LA1511_S+hicyto_9 -6.722222e-02 -0.5631153683 0.428670924
## LA1511_S+lowcyto_9-LA1511_S+hicyto_9 -5.777778e-02 -0.5013180915 0.385762536
## LA1511_S+lowga_9-LA1511_S+hicyto_9 -3.379798e-01 -0.7608788939 0.084919298
## LA1511_S+only_9-LA1511_S+hicyto_9 -2.826098e-01 -0.6275037447 0.062284106
## M058_S+hiaba_9-LA1511_S+hicyto_9 -3.926389e-01 -0.8498297795 0.064552002
## M058_S+hiacc_9-LA1511_S+hicyto_9 -1.758889e-01 -0.6081985110 0.256420733
## M058_S+hicyto_9-LA1511_S+hicyto_9 -1.613889e-01 -0.6185797795 0.295802002
## M058_S+higa_9-LA1511_S+hicyto_9 -4.808889e-01 -0.9131985110 -0.048579267
## M058_S+iaa_9-LA1511_S+hicyto_9 -2.068889e-01 -0.6391985110 0.225420733
## M058_S+lowaba_9-LA1511_S+hicyto_9 -6.088889e-02 -0.4931985110 0.371420733
## M058_S+lowacc_9-LA1511_S+hicyto_9 -9.888889e-02 -0.5311985110 0.333420733
## M058_S+lowcyto_9-LA1511_S+hicyto_9 -4.288889e-02 -0.4751985110 0.389420733
## M058_S+lowga_9-LA1511_S+hicyto_9 -4.038889e-01 -0.8361985110 0.028420733
## M058_S+only_9-LA1511_S+hicyto_9 -3.277261e-01 -0.6726200238 0.017167827
## M248_S+hiaba_9-LA1511_S+hicyto_9 -4.900000e-01 -0.9335403137 -0.046459686
## M248_S+hiacc_9-LA1511_S+hicyto_9 -8.588889e-02 -0.5181985110 0.346420733
## M248_S+hicyto_9-LA1511_S+hicyto_9 2.611111e-02 -0.4310797795 0.483302002
## M248_S+higa_9-LA1511_S+hicyto_9 -2.398889e-01 -0.6721985110 0.192420733
## M248_S+iaa_9-LA1511_S+hicyto_9 -1.438889e-01 -0.5761985110 0.288420733
## M248_S+lowaba_9-LA1511_S+hicyto_9 -5.208889e-01 -0.9531985110 -0.088579267
## M248_S+lowacc_9-LA1511_S+hicyto_9 -9.888889e-02 -0.5424292026 0.344651425
## M248_S+lowcyto_9-LA1511_S+hicyto_9 -1.600000e-01 -0.6035403137 0.283540314
## M248_S+lowga_9-LA1511_S+hicyto_9 -4.868889e-01 -0.9191985110 -0.054579267
## M248_S+only_9-LA1511_S+hicyto_9 -3.284807e-01 -0.6697003953 0.012738944
## LA1511_S+iaa_9-LA1511_S+higa_9 1.720202e-01 -0.2508788939 0.594919298
## LA1511_S+lowaba_9-LA1511_S+higa_9 -3.009091e-02 -0.4411958164 0.381013998
## LA1511_S+lowacc_9-LA1511_S+higa_9 1.825758e-01 -0.2949445538 0.660096069
## LA1511_S+lowcyto_9-LA1511_S+higa_9 1.920202e-01 -0.2308788939 0.614919298
## LA1511_S+lowga_9-LA1511_S+higa_9 -8.818182e-02 -0.4893791273 0.313015491
## LA1511_S+only_9-LA1511_S+higa_9 -3.281184e-02 -0.3507229203 0.285099242
## M058_S+hiaba_9-LA1511_S+higa_9 -1.428409e-01 -0.5800355408 0.294353723
## M058_S+hiacc_9-LA1511_S+higa_9 7.390909e-02 -0.3371958164 0.485013998
## M058_S+hicyto_9-LA1511_S+higa_9 8.840909e-02 -0.3487855408 0.525603723
## M058_S+higa_9-LA1511_S+higa_9 -2.310909e-01 -0.6421958164 0.180013998
## M058_S+iaa_9-LA1511_S+higa_9 4.290909e-02 -0.3681958164 0.454013998
## M058_S+lowaba_9-LA1511_S+higa_9 1.889091e-01 -0.2221958164 0.600013998
## M058_S+lowacc_9-LA1511_S+higa_9 1.509091e-01 -0.2601958164 0.562013998
## M058_S+lowcyto_9-LA1511_S+higa_9 2.069091e-01 -0.2041958164 0.618013998
## M058_S+lowga_9-LA1511_S+higa_9 -1.540909e-01 -0.5651958164 0.257013998
## M058_S+only_9-LA1511_S+higa_9 -7.792812e-02 -0.3958391993 0.239982963
## M248_S+hiaba_9-LA1511_S+higa_9 -2.402020e-01 -0.6631011161 0.182697076
## M248_S+hiacc_9-LA1511_S+higa_9 1.639091e-01 -0.2471958164 0.575013998
## M248_S+hicyto_9-LA1511_S+higa_9 2.759091e-01 -0.1612855408 0.713103723
## M248_S+higa_9-LA1511_S+higa_9 9.909091e-03 -0.4011958164 0.421013998
## M248_S+iaa_9-LA1511_S+higa_9 1.059091e-01 -0.3051958164 0.517013998
## M248_S+lowaba_9-LA1511_S+higa_9 -2.710909e-01 -0.6821958164 0.140013998
## M248_S+lowacc_9-LA1511_S+higa_9 1.509091e-01 -0.2719900050 0.573808187
## M248_S+lowcyto_9-LA1511_S+higa_9 8.979798e-02 -0.3331011161 0.512697076
## M248_S+lowga_9-LA1511_S+higa_9 -2.370909e-01 -0.6481958164 0.174013998
## M248_S+only_9-LA1511_S+higa_9 -7.868275e-02 -0.3926039118 0.235238420
## LA1511_S+lowaba_9-LA1511_S+iaa_9 -2.021111e-01 -0.6344207332 0.230198511
## LA1511_S+lowacc_9-LA1511_S+iaa_9 1.055556e-02 -0.4853375905 0.506448702
## LA1511_S+lowcyto_9-LA1511_S+iaa_9 2.000000e-02 -0.4235403137 0.463540314
## LA1511_S+lowga_9-LA1511_S+iaa_9 -2.602020e-01 -0.6831011161 0.162697076
## LA1511_S+only_9-LA1511_S+iaa_9 -2.048320e-01 -0.5497259670 0.140061884
## M058_S+hiaba_9-LA1511_S+iaa_9 -3.148611e-01 -0.7720520018 0.142329780
## M058_S+hiacc_9-LA1511_S+iaa_9 -9.811111e-02 -0.5304207332 0.334198511
## M058_S+hicyto_9-LA1511_S+iaa_9 -8.361111e-02 -0.5408020018 0.373579780
## M058_S+higa_9-LA1511_S+iaa_9 -4.031111e-01 -0.8354207332 0.029198511
## M058_S+iaa_9-LA1511_S+iaa_9 -1.291111e-01 -0.5614207332 0.303198511
## M058_S+lowaba_9-LA1511_S+iaa_9 1.688889e-02 -0.4154207332 0.449198511
## M058_S+lowacc_9-LA1511_S+iaa_9 -2.111111e-02 -0.4534207332 0.411198511
## M058_S+lowcyto_9-LA1511_S+iaa_9 3.488889e-02 -0.3974207332 0.467198511
## M058_S+lowga_9-LA1511_S+iaa_9 -3.261111e-01 -0.7584207332 0.106198511
## M058_S+only_9-LA1511_S+iaa_9 -2.499483e-01 -0.5948422460 0.094945605
## M248_S+hiaba_9-LA1511_S+iaa_9 -4.122222e-01 -0.8557625359 0.031318091
## M248_S+hiacc_9-LA1511_S+iaa_9 -8.111111e-03 -0.4404207332 0.424198511
## M248_S+hicyto_9-LA1511_S+iaa_9 1.038889e-01 -0.3533020018 0.561079780
## M248_S+higa_9-LA1511_S+iaa_9 -1.621111e-01 -0.5944207332 0.270198511
## M248_S+iaa_9-LA1511_S+iaa_9 -6.611111e-02 -0.4984207332 0.366198511
## M248_S+lowaba_9-LA1511_S+iaa_9 -4.431111e-01 -0.8754207332 -0.010801489
## M248_S+lowacc_9-LA1511_S+iaa_9 -2.111111e-02 -0.4646514248 0.422429203
## M248_S+lowcyto_9-LA1511_S+iaa_9 -8.222222e-02 -0.5257625359 0.361318091
## M248_S+lowga_9-LA1511_S+iaa_9 -4.091111e-01 -0.8414207332 0.023198511
## M248_S+only_9-LA1511_S+iaa_9 -2.507029e-01 -0.5919226175 0.090516722
## LA1511_S+lowacc_9-LA1511_S+lowaba_9 2.126667e-01 -0.2732074033 0.698540737
## LA1511_S+lowcyto_9-LA1511_S+lowaba_9 2.221111e-01 -0.2101985110 0.654420733
## LA1511_S+lowga_9-LA1511_S+lowaba_9 -5.809091e-02 -0.4691958164 0.353013998
## LA1511_S+only_9-LA1511_S+lowaba_9 -2.720930e-03 -0.3330471621 0.327605302
## M058_S+hiaba_9-LA1511_S+lowaba_9 -1.127500e-01 -0.5590538315 0.333553831
## M058_S+hiacc_9-LA1511_S+lowaba_9 1.040000e-01 -0.3167792876 0.524779288
## M058_S+hicyto_9-LA1511_S+lowaba_9 1.185000e-01 -0.3278038315 0.564803831
## M058_S+higa_9-LA1511_S+lowaba_9 -2.010000e-01 -0.6217792876 0.219779288
## M058_S+iaa_9-LA1511_S+lowaba_9 7.300000e-02 -0.3477792876 0.493779288
## M058_S+lowaba_9-LA1511_S+lowaba_9 2.190000e-01 -0.2017792876 0.639779288
## M058_S+lowacc_9-LA1511_S+lowaba_9 1.810000e-01 -0.2397792876 0.601779288
## M058_S+lowcyto_9-LA1511_S+lowaba_9 2.370000e-01 -0.1837792876 0.657779288
## M058_S+lowga_9-LA1511_S+lowaba_9 -1.240000e-01 -0.5447792876 0.296779288
## M058_S+only_9-LA1511_S+lowaba_9 -4.783721e-02 -0.3781634411 0.282489023
## M248_S+hiaba_9-LA1511_S+lowaba_9 -2.101111e-01 -0.6424207332 0.222198511
## M248_S+hiacc_9-LA1511_S+lowaba_9 1.940000e-01 -0.2267792876 0.614779288
## M248_S+hicyto_9-LA1511_S+lowaba_9 3.060000e-01 -0.1403038315 0.752303831
## M248_S+higa_9-LA1511_S+lowaba_9 4.000000e-02 -0.3807792876 0.460779288
## M248_S+iaa_9-LA1511_S+lowaba_9 1.360000e-01 -0.2847792876 0.556779288
## M248_S+lowaba_9-LA1511_S+lowaba_9 -2.410000e-01 -0.6617792876 0.179779288
## M248_S+lowacc_9-LA1511_S+lowaba_9 1.810000e-01 -0.2513096221 0.613309622
## M248_S+lowcyto_9-LA1511_S+lowaba_9 1.198889e-01 -0.3124207332 0.552198511
## M248_S+lowga_9-LA1511_S+lowaba_9 -2.070000e-01 -0.6277792876 0.213779288
## M248_S+only_9-LA1511_S+lowaba_9 -4.859184e-02 -0.3750799108 0.277896237
## LA1511_S+lowcyto_9-LA1511_S+lowacc_9 9.444444e-03 -0.4864487016 0.505337591
## LA1511_S+lowga_9-LA1511_S+lowacc_9 -2.707576e-01 -0.7482778872 0.206762736
## LA1511_S+only_9-LA1511_S+lowacc_9 -2.153876e-01 -0.6254288416 0.194653648
## M058_S+hiaba_9-LA1511_S+lowacc_9 -3.254167e-01 -0.8335559320 0.182722599
## M058_S+hiacc_9-LA1511_S+lowacc_9 -1.086667e-01 -0.5945407366 0.377207403
## M058_S+hicyto_9-LA1511_S+lowacc_9 -9.416667e-02 -0.6023059320 0.413972599
## M058_S+higa_9-LA1511_S+lowacc_9 -4.136667e-01 -0.8995407366 0.072207403
## M058_S+iaa_9-LA1511_S+lowacc_9 -1.396667e-01 -0.6255407366 0.346207403
## M058_S+lowaba_9-LA1511_S+lowacc_9 6.333333e-03 -0.4795407366 0.492207403
## M058_S+lowacc_9-LA1511_S+lowacc_9 -3.166667e-02 -0.5175407366 0.454207403
## M058_S+lowcyto_9-LA1511_S+lowacc_9 2.433333e-02 -0.4615407366 0.510207403
## M058_S+lowga_9-LA1511_S+lowacc_9 -3.366667e-01 -0.8225407366 0.149207403
## M058_S+only_9-LA1511_S+lowacc_9 -2.605039e-01 -0.6705451207 0.149537369
## M248_S+hiaba_9-LA1511_S+lowacc_9 -4.227778e-01 -0.9186709239 0.073115368
## M248_S+hiacc_9-LA1511_S+lowacc_9 -1.866667e-02 -0.5045407366 0.467207403
## M248_S+hicyto_9-LA1511_S+lowacc_9 9.333333e-02 -0.4148059320 0.601472599
## M248_S+higa_9-LA1511_S+lowacc_9 -1.726667e-01 -0.6585407366 0.313207403
## M248_S+iaa_9-LA1511_S+lowacc_9 -7.666667e-02 -0.5625407366 0.409207403
## M248_S+lowaba_9-LA1511_S+lowacc_9 -4.536667e-01 -0.9395407366 0.032207403
## M248_S+lowacc_9-LA1511_S+lowacc_9 -3.166667e-02 -0.5275598128 0.464226479
## M248_S+lowcyto_9-LA1511_S+lowacc_9 -9.277778e-02 -0.5886709239 0.403115368
## M248_S+lowga_9-LA1511_S+lowacc_9 -4.196667e-01 -0.9055407366 0.066207403
## M248_S+only_9-LA1511_S+lowacc_9 -2.612585e-01 -0.6682141096 0.145697103
## LA1511_S+lowga_9-LA1511_S+lowcyto_9 -2.802020e-01 -0.7031011161 0.142697076
## LA1511_S+only_9-LA1511_S+lowcyto_9 -2.248320e-01 -0.5697259670 0.120061884
## M058_S+hiaba_9-LA1511_S+lowcyto_9 -3.348611e-01 -0.7920520018 0.122329780
## M058_S+hiacc_9-LA1511_S+lowcyto_9 -1.181111e-01 -0.5504207332 0.314198511
## M058_S+hicyto_9-LA1511_S+lowcyto_9 -1.036111e-01 -0.5608020018 0.353579780
## M058_S+higa_9-LA1511_S+lowcyto_9 -4.231111e-01 -0.8554207332 0.009198511
## M058_S+iaa_9-LA1511_S+lowcyto_9 -1.491111e-01 -0.5814207332 0.283198511
## M058_S+lowaba_9-LA1511_S+lowcyto_9 -3.111111e-03 -0.4354207332 0.429198511
## M058_S+lowacc_9-LA1511_S+lowcyto_9 -4.111111e-02 -0.4734207332 0.391198511
## M058_S+lowcyto_9-LA1511_S+lowcyto_9 1.488889e-02 -0.4174207332 0.447198511
## M058_S+lowga_9-LA1511_S+lowcyto_9 -3.461111e-01 -0.7784207332 0.086198511
## M058_S+only_9-LA1511_S+lowcyto_9 -2.699483e-01 -0.6148422460 0.074945605
## M248_S+hiaba_9-LA1511_S+lowcyto_9 -4.322222e-01 -0.8757625359 0.011318091
## M248_S+hiacc_9-LA1511_S+lowcyto_9 -2.811111e-02 -0.4604207332 0.404198511
## M248_S+hicyto_9-LA1511_S+lowcyto_9 8.388889e-02 -0.3733020018 0.541079780
## M248_S+higa_9-LA1511_S+lowcyto_9 -1.821111e-01 -0.6144207332 0.250198511
## M248_S+iaa_9-LA1511_S+lowcyto_9 -8.611111e-02 -0.5184207332 0.346198511
## M248_S+lowaba_9-LA1511_S+lowcyto_9 -4.631111e-01 -0.8954207332 -0.030801489
## M248_S+lowacc_9-LA1511_S+lowcyto_9 -4.111111e-02 -0.4846514248 0.402429203
## M248_S+lowcyto_9-LA1511_S+lowcyto_9 -1.022222e-01 -0.5457625359 0.341318091
## M248_S+lowga_9-LA1511_S+lowcyto_9 -4.291111e-01 -0.8614207332 0.003198511
## M248_S+only_9-LA1511_S+lowcyto_9 -2.707029e-01 -0.6119226175 0.070516722
## LA1511_S+only_9-LA1511_S+lowga_9 5.536998e-02 -0.2625411021 0.373281060
## M058_S+hiaba_9-LA1511_S+lowga_9 -5.465909e-02 -0.4918537226 0.382535541
## M058_S+hiacc_9-LA1511_S+lowga_9 1.620909e-01 -0.2490139983 0.573195816
## M058_S+hicyto_9-LA1511_S+lowga_9 1.765909e-01 -0.2606037226 0.613785541
## M058_S+higa_9-LA1511_S+lowga_9 -1.429091e-01 -0.5540139983 0.268195816
## M058_S+iaa_9-LA1511_S+lowga_9 1.310909e-01 -0.2800139983 0.542195816
## M058_S+lowaba_9-LA1511_S+lowga_9 2.770909e-01 -0.1340139983 0.688195816
## M058_S+lowacc_9-LA1511_S+lowga_9 2.390909e-01 -0.1720139983 0.650195816
## M058_S+lowcyto_9-LA1511_S+lowga_9 2.950909e-01 -0.1160139983 0.706195816
## M058_S+lowga_9-LA1511_S+lowga_9 -6.590909e-02 -0.4770139983 0.345195816
## M058_S+only_9-LA1511_S+lowga_9 1.025370e-02 -0.3076573812 0.328164781
## M248_S+hiaba_9-LA1511_S+lowga_9 -1.520202e-01 -0.5749192980 0.270878894
## M248_S+hiacc_9-LA1511_S+lowga_9 2.520909e-01 -0.1590139983 0.663195816
## M248_S+hicyto_9-LA1511_S+lowga_9 3.640909e-01 -0.0731037226 0.801285541
## M248_S+higa_9-LA1511_S+lowga_9 9.809091e-02 -0.3130139983 0.509195816
## M248_S+iaa_9-LA1511_S+lowga_9 1.940909e-01 -0.2170139983 0.605195816
## M248_S+lowaba_9-LA1511_S+lowga_9 -1.829091e-01 -0.5940139983 0.228195816
## M248_S+lowacc_9-LA1511_S+lowga_9 2.390909e-01 -0.1838081868 0.661990005
## M248_S+lowcyto_9-LA1511_S+lowga_9 1.779798e-01 -0.2449192980 0.600878894
## M248_S+lowga_9-LA1511_S+lowga_9 -1.489091e-01 -0.5600139983 0.262195816
## M248_S+only_9-LA1511_S+lowga_9 9.499072e-03 -0.3044220936 0.323420238
## M058_S+hiaba_9-LA1511_S+only_9 -1.100291e-01 -0.4723097904 0.252251651
## M058_S+hiacc_9-LA1511_S+only_9 1.067209e-01 -0.2236053016 0.437047162
## M058_S+hicyto_9-LA1511_S+only_9 1.212209e-01 -0.2410597904 0.483501651
## M058_S+higa_9-LA1511_S+only_9 -1.982791e-01 -0.5286053016 0.132047162
## M058_S+iaa_9-LA1511_S+only_9 7.572093e-02 -0.2546053016 0.406047162
## M058_S+lowaba_9-LA1511_S+only_9 2.217209e-01 -0.1086053016 0.552047162
## M058_S+lowacc_9-LA1511_S+only_9 1.837209e-01 -0.1466053016 0.514047162
## M058_S+lowcyto_9-LA1511_S+only_9 2.397209e-01 -0.0906053016 0.570047162
## M058_S+lowga_9-LA1511_S+only_9 -1.212791e-01 -0.4516053016 0.209047162
## M058_S+only_9-LA1511_S+only_9 -4.511628e-02 -0.2480340702 0.157801512
## M248_S+hiaba_9-LA1511_S+only_9 -2.073902e-01 -0.5522841065 0.137503745
## M248_S+hiacc_9-LA1511_S+only_9 1.967209e-01 -0.1336053016 0.527047162
## M248_S+hicyto_9-LA1511_S+only_9 3.087209e-01 -0.0535597904 0.671001651
## M248_S+higa_9-LA1511_S+only_9 4.272093e-02 -0.2876053016 0.373047162
## M248_S+iaa_9-LA1511_S+only_9 1.387209e-01 -0.1916053016 0.469047162
## M248_S+lowaba_9-LA1511_S+only_9 -2.382791e-01 -0.5686053016 0.092047162
## M248_S+lowacc_9-LA1511_S+only_9 1.837209e-01 -0.1611729954 0.528614856
## M248_S+lowcyto_9-LA1511_S+only_9 1.226098e-01 -0.2222841065 0.467503745
## M248_S+lowga_9-LA1511_S+only_9 -2.042791e-01 -0.5346053016 0.126047162
## M248_S+only_9-LA1511_S+only_9 -4.587091e-02 -0.2424788235 0.150737011
## M058_S+hiacc_9-M058_S+hiaba_9 2.167500e-01 -0.2295538315 0.663053831
## M058_S+hicyto_9-M058_S+hiaba_9 2.312500e-01 -0.2391955453 0.701695545
## M058_S+higa_9-M058_S+hiaba_9 -8.825000e-02 -0.5345538315 0.358053831
## M058_S+iaa_9-M058_S+hiaba_9 1.857500e-01 -0.2605538315 0.632053831
## M058_S+lowaba_9-M058_S+hiaba_9 3.317500e-01 -0.1145538315 0.778053831
## M058_S+lowacc_9-M058_S+hiaba_9 2.937500e-01 -0.1525538315 0.740053831
## M058_S+lowcyto_9-M058_S+hiaba_9 3.497500e-01 -0.0965538315 0.796053831
## M058_S+lowga_9-M058_S+hiaba_9 -1.125000e-02 -0.4575538315 0.435053831
## M058_S+only_9-M058_S+hiaba_9 6.491279e-02 -0.2973679299 0.427193511
## M248_S+hiaba_9-M058_S+hiaba_9 -9.736111e-02 -0.5545520018 0.359829780
## M248_S+hiacc_9-M058_S+hiaba_9 3.067500e-01 -0.1395538315 0.753053831
## M248_S+hicyto_9-M058_S+hiaba_9 4.187500e-01 -0.0516955453 0.889195545
## M248_S+higa_9-M058_S+hiaba_9 1.527500e-01 -0.2935538315 0.599053831
## M248_S+iaa_9-M058_S+hiaba_9 2.487500e-01 -0.1975538315 0.695053831
## M248_S+lowaba_9-M058_S+hiaba_9 -1.282500e-01 -0.5745538315 0.318053831
## M248_S+lowacc_9-M058_S+hiaba_9 2.937500e-01 -0.1634408906 0.750940891
## M248_S+lowcyto_9-M058_S+hiaba_9 2.326389e-01 -0.2245520018 0.689829780
## M248_S+lowga_9-M058_S+hiaba_9 -9.425000e-02 -0.5405538315 0.352053831
## M248_S+only_9-M058_S+hiaba_9 6.415816e-02 -0.2946264011 0.422942728
## M058_S+hicyto_9-M058_S+hiacc_9 1.450000e-02 -0.4318038315 0.460803831
## M058_S+higa_9-M058_S+hiacc_9 -3.050000e-01 -0.7257792876 0.115779288
## M058_S+iaa_9-M058_S+hiacc_9 -3.100000e-02 -0.4517792876 0.389779288
## M058_S+lowaba_9-M058_S+hiacc_9 1.150000e-01 -0.3057792876 0.535779288
## M058_S+lowacc_9-M058_S+hiacc_9 7.700000e-02 -0.3437792876 0.497779288
## M058_S+lowcyto_9-M058_S+hiacc_9 1.330000e-01 -0.2877792876 0.553779288
## M058_S+lowga_9-M058_S+hiacc_9 -2.280000e-01 -0.6487792876 0.192779288
## M058_S+only_9-M058_S+hiacc_9 -1.518372e-01 -0.4821634411 0.178489023
## M248_S+hiaba_9-M058_S+hiacc_9 -3.141111e-01 -0.7464207332 0.118198511
## M248_S+hiacc_9-M058_S+hiacc_9 9.000000e-02 -0.3307792876 0.510779288
## M248_S+hicyto_9-M058_S+hiacc_9 2.020000e-01 -0.2443038315 0.648303831
## M248_S+higa_9-M058_S+hiacc_9 -6.400000e-02 -0.4847792876 0.356779288
## M248_S+iaa_9-M058_S+hiacc_9 3.200000e-02 -0.3887792876 0.452779288
## M248_S+lowaba_9-M058_S+hiacc_9 -3.450000e-01 -0.7657792876 0.075779288
## M248_S+lowacc_9-M058_S+hiacc_9 7.700000e-02 -0.3553096221 0.509309622
## M248_S+lowcyto_9-M058_S+hiacc_9 1.588889e-02 -0.4164207332 0.448198511
## M248_S+lowga_9-M058_S+hiacc_9 -3.110000e-01 -0.7317792876 0.109779288
## M248_S+only_9-M058_S+hiacc_9 -1.525918e-01 -0.4790799108 0.173896237
## M058_S+higa_9-M058_S+hicyto_9 -3.195000e-01 -0.7658038315 0.126803831
## M058_S+iaa_9-M058_S+hicyto_9 -4.550000e-02 -0.4918038315 0.400803831
## M058_S+lowaba_9-M058_S+hicyto_9 1.005000e-01 -0.3458038315 0.546803831
## M058_S+lowacc_9-M058_S+hicyto_9 6.250000e-02 -0.3838038315 0.508803831
## M058_S+lowcyto_9-M058_S+hicyto_9 1.185000e-01 -0.3278038315 0.564803831
## M058_S+lowga_9-M058_S+hicyto_9 -2.425000e-01 -0.6888038315 0.203803831
## M058_S+only_9-M058_S+hicyto_9 -1.663372e-01 -0.5286179299 0.195943511
## M248_S+hiaba_9-M058_S+hicyto_9 -3.286111e-01 -0.7858020018 0.128579780
## M248_S+hiacc_9-M058_S+hicyto_9 7.550000e-02 -0.3708038315 0.521803831
## M248_S+hicyto_9-M058_S+hicyto_9 1.875000e-01 -0.2829455453 0.657945545
## M248_S+higa_9-M058_S+hicyto_9 -7.850000e-02 -0.5248038315 0.367803831
## M248_S+iaa_9-M058_S+hicyto_9 1.750000e-02 -0.4288038315 0.463803831
## M248_S+lowaba_9-M058_S+hicyto_9 -3.595000e-01 -0.8058038315 0.086803831
## M248_S+lowacc_9-M058_S+hicyto_9 6.250000e-02 -0.3946908906 0.519690891
## M248_S+lowcyto_9-M058_S+hicyto_9 1.388889e-03 -0.4558020018 0.458579780
## M248_S+lowga_9-M058_S+hicyto_9 -3.255000e-01 -0.7718038315 0.120803831
## M248_S+only_9-M058_S+hicyto_9 -1.670918e-01 -0.5258764011 0.191692728
## M058_S+iaa_9-M058_S+higa_9 2.740000e-01 -0.1467792876 0.694779288
## M058_S+lowaba_9-M058_S+higa_9 4.200000e-01 -0.0007792876 0.840779288
## M058_S+lowacc_9-M058_S+higa_9 3.820000e-01 -0.0387792876 0.802779288
## M058_S+lowcyto_9-M058_S+higa_9 4.380000e-01 0.0172207124 0.858779288
## M058_S+lowga_9-M058_S+higa_9 7.700000e-02 -0.3437792876 0.497779288
## M058_S+only_9-M058_S+higa_9 1.531628e-01 -0.1771634411 0.483489023
## M248_S+hiaba_9-M058_S+higa_9 -9.111111e-03 -0.4414207332 0.423198511
## M248_S+hiacc_9-M058_S+higa_9 3.950000e-01 -0.0257792876 0.815779288
## M248_S+hicyto_9-M058_S+higa_9 5.070000e-01 0.0606961685 0.953303831
## M248_S+higa_9-M058_S+higa_9 2.410000e-01 -0.1797792876 0.661779288
## M248_S+iaa_9-M058_S+higa_9 3.370000e-01 -0.0837792876 0.757779288
## M248_S+lowaba_9-M058_S+higa_9 -4.000000e-02 -0.4607792876 0.380779288
## M248_S+lowacc_9-M058_S+higa_9 3.820000e-01 -0.0503096221 0.814309622
## M248_S+lowcyto_9-M058_S+higa_9 3.208889e-01 -0.1114207332 0.753198511
## M248_S+lowga_9-M058_S+higa_9 -6.000000e-03 -0.4267792876 0.414779288
## M248_S+only_9-M058_S+higa_9 1.524082e-01 -0.1740799108 0.478896237
## M058_S+lowaba_9-M058_S+iaa_9 1.460000e-01 -0.2747792876 0.566779288
## M058_S+lowacc_9-M058_S+iaa_9 1.080000e-01 -0.3127792876 0.528779288
## M058_S+lowcyto_9-M058_S+iaa_9 1.640000e-01 -0.2567792876 0.584779288
## M058_S+lowga_9-M058_S+iaa_9 -1.970000e-01 -0.6177792876 0.223779288
## M058_S+only_9-M058_S+iaa_9 -1.208372e-01 -0.4511634411 0.209489023
## M248_S+hiaba_9-M058_S+iaa_9 -2.831111e-01 -0.7154207332 0.149198511
## M248_S+hiacc_9-M058_S+iaa_9 1.210000e-01 -0.2997792876 0.541779288
## M248_S+hicyto_9-M058_S+iaa_9 2.330000e-01 -0.2133038315 0.679303831
## M248_S+higa_9-M058_S+iaa_9 -3.300000e-02 -0.4537792876 0.387779288
## M248_S+iaa_9-M058_S+iaa_9 6.300000e-02 -0.3577792876 0.483779288
## M248_S+lowaba_9-M058_S+iaa_9 -3.140000e-01 -0.7347792876 0.106779288
## M248_S+lowacc_9-M058_S+iaa_9 1.080000e-01 -0.3243096221 0.540309622
## M248_S+lowcyto_9-M058_S+iaa_9 4.688889e-02 -0.3854207332 0.479198511
## M248_S+lowga_9-M058_S+iaa_9 -2.800000e-01 -0.7007792876 0.140779288
## M248_S+only_9-M058_S+iaa_9 -1.215918e-01 -0.4480799108 0.204896237
## M058_S+lowacc_9-M058_S+lowaba_9 -3.800000e-02 -0.4587792876 0.382779288
## M058_S+lowcyto_9-M058_S+lowaba_9 1.800000e-02 -0.4027792876 0.438779288
## M058_S+lowga_9-M058_S+lowaba_9 -3.430000e-01 -0.7637792876 0.077779288
## M058_S+only_9-M058_S+lowaba_9 -2.668372e-01 -0.5971634411 0.063489023
## M248_S+hiaba_9-M058_S+lowaba_9 -4.291111e-01 -0.8614207332 0.003198511
## M248_S+hiacc_9-M058_S+lowaba_9 -2.500000e-02 -0.4457792876 0.395779288
## M248_S+hicyto_9-M058_S+lowaba_9 8.700000e-02 -0.3593038315 0.533303831
## M248_S+higa_9-M058_S+lowaba_9 -1.790000e-01 -0.5997792876 0.241779288
## M248_S+iaa_9-M058_S+lowaba_9 -8.300000e-02 -0.5037792876 0.337779288
## M248_S+lowaba_9-M058_S+lowaba_9 -4.600000e-01 -0.8807792876 -0.039220712
## M248_S+lowacc_9-M058_S+lowaba_9 -3.800000e-02 -0.4703096221 0.394309622
## M248_S+lowcyto_9-M058_S+lowaba_9 -9.911111e-02 -0.5314207332 0.333198511
## M248_S+lowga_9-M058_S+lowaba_9 -4.260000e-01 -0.8467792876 -0.005220712
## M248_S+only_9-M058_S+lowaba_9 -2.675918e-01 -0.5940799108 0.058896237
## M058_S+lowcyto_9-M058_S+lowacc_9 5.600000e-02 -0.3647792876 0.476779288
## M058_S+lowga_9-M058_S+lowacc_9 -3.050000e-01 -0.7257792876 0.115779288
## M058_S+only_9-M058_S+lowacc_9 -2.288372e-01 -0.5591634411 0.101489023
## M248_S+hiaba_9-M058_S+lowacc_9 -3.911111e-01 -0.8234207332 0.041198511
## M248_S+hiacc_9-M058_S+lowacc_9 1.300000e-02 -0.4077792876 0.433779288
## M248_S+hicyto_9-M058_S+lowacc_9 1.250000e-01 -0.3213038315 0.571303831
## M248_S+higa_9-M058_S+lowacc_9 -1.410000e-01 -0.5617792876 0.279779288
## M248_S+iaa_9-M058_S+lowacc_9 -4.500000e-02 -0.4657792876 0.375779288
## M248_S+lowaba_9-M058_S+lowacc_9 -4.220000e-01 -0.8427792876 -0.001220712
## M248_S+lowacc_9-M058_S+lowacc_9 -3.552714e-15 -0.4323096221 0.432309622
## M248_S+lowcyto_9-M058_S+lowacc_9 -6.111111e-02 -0.4934207332 0.371198511
## M248_S+lowga_9-M058_S+lowacc_9 -3.880000e-01 -0.8087792876 0.032779288
## M248_S+only_9-M058_S+lowacc_9 -2.295918e-01 -0.5560799108 0.096896237
## M058_S+lowga_9-M058_S+lowcyto_9 -3.610000e-01 -0.7817792876 0.059779288
## M058_S+only_9-M058_S+lowcyto_9 -2.848372e-01 -0.6151634411 0.045489023
## M248_S+hiaba_9-M058_S+lowcyto_9 -4.471111e-01 -0.8794207332 -0.014801489
## M248_S+hiacc_9-M058_S+lowcyto_9 -4.300000e-02 -0.4637792876 0.377779288
## M248_S+hicyto_9-M058_S+lowcyto_9 6.900000e-02 -0.3773038315 0.515303831
## M248_S+higa_9-M058_S+lowcyto_9 -1.970000e-01 -0.6177792876 0.223779288
## M248_S+iaa_9-M058_S+lowcyto_9 -1.010000e-01 -0.5217792876 0.319779288
## M248_S+lowaba_9-M058_S+lowcyto_9 -4.780000e-01 -0.8987792876 -0.057220712
## M248_S+lowacc_9-M058_S+lowcyto_9 -5.600000e-02 -0.4883096221 0.376309622
## M248_S+lowcyto_9-M058_S+lowcyto_9 -1.171111e-01 -0.5494207332 0.315198511
## M248_S+lowga_9-M058_S+lowcyto_9 -4.440000e-01 -0.8647792876 -0.023220712
## M248_S+only_9-M058_S+lowcyto_9 -2.855918e-01 -0.6120799108 0.040896237
## M058_S+only_9-M058_S+lowga_9 7.616279e-02 -0.2541634411 0.406489023
## M248_S+hiaba_9-M058_S+lowga_9 -8.611111e-02 -0.5184207332 0.346198511
## M248_S+hiacc_9-M058_S+lowga_9 3.180000e-01 -0.1027792876 0.738779288
## M248_S+hicyto_9-M058_S+lowga_9 4.300000e-01 -0.0163038315 0.876303831
## M248_S+higa_9-M058_S+lowga_9 1.640000e-01 -0.2567792876 0.584779288
## M248_S+iaa_9-M058_S+lowga_9 2.600000e-01 -0.1607792876 0.680779288
## M248_S+lowaba_9-M058_S+lowga_9 -1.170000e-01 -0.5377792876 0.303779288
## M248_S+lowacc_9-M058_S+lowga_9 3.050000e-01 -0.1273096221 0.737309622
## M248_S+lowcyto_9-M058_S+lowga_9 2.438889e-01 -0.1884207332 0.676198511
## M248_S+lowga_9-M058_S+lowga_9 -8.300000e-02 -0.5037792876 0.337779288
## M248_S+only_9-M058_S+lowga_9 7.540816e-02 -0.2510799108 0.401896237
## M248_S+hiaba_9-M058_S+only_9 -1.622739e-01 -0.5071678274 0.182620024
## M248_S+hiacc_9-M058_S+only_9 2.418372e-01 -0.0884890225 0.572163441
## M248_S+hicyto_9-M058_S+only_9 3.538372e-01 -0.0084435113 0.716117930
## M248_S+higa_9-M058_S+only_9 8.783721e-02 -0.2424890225 0.418163441
## M248_S+iaa_9-M058_S+only_9 1.838372e-01 -0.1464890225 0.514163441
## M248_S+lowaba_9-M058_S+only_9 -1.931628e-01 -0.5234890225 0.137163441
## M248_S+lowacc_9-M058_S+only_9 2.288372e-01 -0.1160567163 0.573731135
## M248_S+lowcyto_9-M058_S+only_9 1.677261e-01 -0.1771678274 0.512620024
## M248_S+lowga_9-M058_S+only_9 -1.591628e-01 -0.4894890225 0.171163441
## M248_S+only_9-M058_S+only_9 -7.546274e-04 -0.1973625445 0.195853290
## M248_S+hiacc_9-M248_S+hiaba_9 4.041111e-01 -0.0281985110 0.836420733
## M248_S+hicyto_9-M248_S+hiaba_9 5.161111e-01 0.0589202205 0.973302002
## M248_S+higa_9-M248_S+hiaba_9 2.501111e-01 -0.1821985110 0.682420733
## M248_S+iaa_9-M248_S+hiaba_9 3.461111e-01 -0.0861985110 0.778420733
## M248_S+lowaba_9-M248_S+hiaba_9 -3.088889e-02 -0.4631985110 0.401420733
## M248_S+lowacc_9-M248_S+hiaba_9 3.911111e-01 -0.0524292026 0.834651425
## M248_S+lowcyto_9-M248_S+hiaba_9 3.300000e-01 -0.1135403137 0.773540314
## M248_S+lowga_9-M248_S+hiaba_9 3.111111e-03 -0.4291985110 0.435420733
## M248_S+only_9-M248_S+hiaba_9 1.615193e-01 -0.1797003953 0.502738944
## M248_S+hicyto_9-M248_S+hiacc_9 1.120000e-01 -0.3343038315 0.558303831
## M248_S+higa_9-M248_S+hiacc_9 -1.540000e-01 -0.5747792876 0.266779288
## M248_S+iaa_9-M248_S+hiacc_9 -5.800000e-02 -0.4787792876 0.362779288
## M248_S+lowaba_9-M248_S+hiacc_9 -4.350000e-01 -0.8557792876 -0.014220712
## M248_S+lowacc_9-M248_S+hiacc_9 -1.300000e-02 -0.4453096221 0.419309622
## M248_S+lowcyto_9-M248_S+hiacc_9 -7.411111e-02 -0.5064207332 0.358198511
## M248_S+lowga_9-M248_S+hiacc_9 -4.010000e-01 -0.8217792876 0.019779288
## M248_S+only_9-M248_S+hiacc_9 -2.425918e-01 -0.5690799108 0.083896237
## M248_S+higa_9-M248_S+hicyto_9 -2.660000e-01 -0.7123038315 0.180303831
## M248_S+iaa_9-M248_S+hicyto_9 -1.700000e-01 -0.6163038315 0.276303831
## M248_S+lowaba_9-M248_S+hicyto_9 -5.470000e-01 -0.9933038315 -0.100696169
## M248_S+lowacc_9-M248_S+hicyto_9 -1.250000e-01 -0.5821908906 0.332190891
## M248_S+lowcyto_9-M248_S+hicyto_9 -1.861111e-01 -0.6433020018 0.271079780
## M248_S+lowga_9-M248_S+hicyto_9 -5.130000e-01 -0.9593038315 -0.066696169
## M248_S+only_9-M248_S+hicyto_9 -3.545918e-01 -0.7133764011 0.004192728
## M248_S+iaa_9-M248_S+higa_9 9.600000e-02 -0.3247792876 0.516779288
## M248_S+lowaba_9-M248_S+higa_9 -2.810000e-01 -0.7017792876 0.139779288
## M248_S+lowacc_9-M248_S+higa_9 1.410000e-01 -0.2913096221 0.573309622
## M248_S+lowcyto_9-M248_S+higa_9 7.988889e-02 -0.3524207332 0.512198511
## M248_S+lowga_9-M248_S+higa_9 -2.470000e-01 -0.6677792876 0.173779288
## M248_S+only_9-M248_S+higa_9 -8.859184e-02 -0.4150799108 0.237896237
## M248_S+lowaba_9-M248_S+iaa_9 -3.770000e-01 -0.7977792876 0.043779288
## M248_S+lowacc_9-M248_S+iaa_9 4.500000e-02 -0.3873096221 0.477309622
## M248_S+lowcyto_9-M248_S+iaa_9 -1.611111e-02 -0.4484207332 0.416198511
## M248_S+lowga_9-M248_S+iaa_9 -3.430000e-01 -0.7637792876 0.077779288
## M248_S+only_9-M248_S+iaa_9 -1.845918e-01 -0.5110799108 0.141896237
## M248_S+lowacc_9-M248_S+lowaba_9 4.220000e-01 -0.0103096221 0.854309622
## M248_S+lowcyto_9-M248_S+lowaba_9 3.608889e-01 -0.0714207332 0.793198511
## M248_S+lowga_9-M248_S+lowaba_9 3.400000e-02 -0.3867792876 0.454779288
## M248_S+only_9-M248_S+lowaba_9 1.924082e-01 -0.1340799108 0.518896237
## M248_S+lowcyto_9-M248_S+lowacc_9 -6.111111e-02 -0.5046514248 0.382429203
## M248_S+lowga_9-M248_S+lowacc_9 -3.880000e-01 -0.8203096221 0.044309622
## M248_S+only_9-M248_S+lowacc_9 -2.295918e-01 -0.5708115064 0.111627833
## M248_S+lowga_9-M248_S+lowcyto_9 -3.268889e-01 -0.7591985110 0.105420733
## M248_S+only_9-M248_S+lowcyto_9 -1.684807e-01 -0.5097003953 0.172738944
## M248_S+only_9-M248_S+lowga_9 1.584082e-01 -0.1680799108 0.484896237
## p adj
## LA1511_S+hiacc_9-LA1511_S+hiaba_9 0.9998516
## LA1511_S+hicyto_9-LA1511_S+hiaba_9 0.5892028
## LA1511_S+higa_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+iaa_9-LA1511_S+hiaba_9 0.9441829
## LA1511_S+lowaba_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+hiaba_9 0.9704971
## LA1511_S+lowcyto_9-LA1511_S+hiaba_9 0.8874637
## LA1511_S+lowga_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+only_9-LA1511_S+hiaba_9 1.0000000
## M058_S+hiaba_9-LA1511_S+hiaba_9 1.0000000
## M058_S+hiacc_9-LA1511_S+hiaba_9 0.9998928
## M058_S+hicyto_9-LA1511_S+hiaba_9 0.9998075
## M058_S+higa_9-LA1511_S+hiaba_9 1.0000000
## M058_S+iaa_9-LA1511_S+hiaba_9 0.9999976
## M058_S+lowaba_9-LA1511_S+hiaba_9 0.8763571
## M058_S+lowacc_9-LA1511_S+hiaba_9 0.9714531
## M058_S+lowcyto_9-LA1511_S+hiaba_9 0.7966758
## M058_S+lowga_9-LA1511_S+hiaba_9 1.0000000
## M058_S+only_9-LA1511_S+hiaba_9 1.0000000
## M248_S+hiaba_9-LA1511_S+hiaba_9 1.0000000
## M248_S+hiacc_9-LA1511_S+hiaba_9 0.9493453
## M248_S+hicyto_9-LA1511_S+hiaba_9 0.4854466
## M248_S+higa_9-LA1511_S+hiaba_9 1.0000000
## M248_S+iaa_9-LA1511_S+hiaba_9 0.9981313
## M248_S+lowaba_9-LA1511_S+hiaba_9 0.9999940
## M248_S+lowacc_9-LA1511_S+hiaba_9 0.9779341
## M248_S+lowcyto_9-LA1511_S+hiaba_9 0.9996562
## M248_S+lowga_9-LA1511_S+hiaba_9 1.0000000
## M248_S+only_9-LA1511_S+hiaba_9 1.0000000
## LA1511_S+hicyto_9-LA1511_S+hiacc_9 0.9999990
## LA1511_S+higa_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+iaa_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+hiacc_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+hiacc_9 0.9998024
## LA1511_S+only_9-LA1511_S+hiacc_9 0.9999964
## M058_S+hiaba_9-LA1511_S+hiacc_9 0.9947075
## M058_S+hiacc_9-LA1511_S+hiacc_9 1.0000000
## M058_S+hicyto_9-LA1511_S+hiacc_9 1.0000000
## M058_S+higa_9-LA1511_S+hiacc_9 0.7286040
## M058_S+iaa_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowaba_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowacc_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+hiacc_9 1.0000000
## M058_S+lowga_9-LA1511_S+hiacc_9 0.9811059
## M058_S+only_9-LA1511_S+hiacc_9 0.9988972
## M248_S+hiaba_9-LA1511_S+hiacc_9 0.7156588
## M248_S+hiacc_9-LA1511_S+hiacc_9 1.0000000
## M248_S+hicyto_9-LA1511_S+hiacc_9 0.9999819
## M248_S+higa_9-LA1511_S+hiacc_9 1.0000000
## M248_S+iaa_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowaba_9-LA1511_S+hiacc_9 0.4816566
## M248_S+lowacc_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+hiacc_9 1.0000000
## M248_S+lowga_9-LA1511_S+hiacc_9 0.6936668
## M248_S+only_9-LA1511_S+hiacc_9 0.9986537
## LA1511_S+higa_9-LA1511_S+hicyto_9 0.9187781
## LA1511_S+iaa_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+hicyto_9 0.8119297
## LA1511_S+lowacc_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+hicyto_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+hicyto_9 0.3742432
## LA1511_S+only_9-LA1511_S+hicyto_9 0.3205774
## M058_S+hiaba_9-LA1511_S+hicyto_9 0.2293814
## M058_S+hiacc_9-LA1511_S+hicyto_9 0.9996168
## M058_S+hicyto_9-LA1511_S+hicyto_9 0.9999753
## M058_S+higa_9-LA1511_S+hicyto_9 0.0109449
## M058_S+iaa_9-LA1511_S+hicyto_9 0.9943362
## M058_S+lowaba_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowacc_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+hicyto_9 1.0000000
## M058_S+lowga_9-LA1511_S+hicyto_9 0.1078019
## M058_S+only_9-LA1511_S+hicyto_9 0.0902587
## M248_S+hiaba_9-LA1511_S+hicyto_9 0.0122243
## M248_S+hiacc_9-LA1511_S+hicyto_9 1.0000000
## M248_S+hicyto_9-LA1511_S+hicyto_9 1.0000000
## M248_S+higa_9-LA1511_S+hicyto_9 0.9590748
## M248_S+iaa_9-LA1511_S+hicyto_9 0.9999927
## M248_S+lowaba_9-LA1511_S+hicyto_9 0.0026454
## M248_S+lowacc_9-LA1511_S+hicyto_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+hicyto_9 0.9999617
## M248_S+lowga_9-LA1511_S+hicyto_9 0.0089264
## M248_S+only_9-LA1511_S+hicyto_9 0.0782704
## LA1511_S+iaa_9-LA1511_S+higa_9 0.9996184
## LA1511_S+lowaba_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowacc_9-LA1511_S+higa_9 0.9998798
## LA1511_S+lowcyto_9-LA1511_S+higa_9 0.9974949
## LA1511_S+lowga_9-LA1511_S+higa_9 1.0000000
## LA1511_S+only_9-LA1511_S+higa_9 1.0000000
## M058_S+hiaba_9-LA1511_S+higa_9 0.9999951
## M058_S+hiacc_9-LA1511_S+higa_9 1.0000000
## M058_S+hicyto_9-LA1511_S+higa_9 1.0000000
## M058_S+higa_9-LA1511_S+higa_9 0.9524848
## M058_S+iaa_9-LA1511_S+higa_9 1.0000000
## M058_S+lowaba_9-LA1511_S+higa_9 0.9969696
## M058_S+lowacc_9-LA1511_S+higa_9 0.9999457
## M058_S+lowcyto_9-LA1511_S+higa_9 0.9882754
## M058_S+lowga_9-LA1511_S+higa_9 0.9999181
## M058_S+only_9-LA1511_S+higa_9 1.0000000
## M248_S+hiaba_9-LA1511_S+higa_9 0.9465819
## M248_S+hiacc_9-LA1511_S+higa_9 0.9997354
## M248_S+hicyto_9-LA1511_S+higa_9 0.8481549
## M248_S+higa_9-LA1511_S+higa_9 1.0000000
## M248_S+iaa_9-LA1511_S+higa_9 1.0000000
## M248_S+lowaba_9-LA1511_S+higa_9 0.7827591
## M248_S+lowacc_9-LA1511_S+higa_9 0.9999692
## M248_S+lowcyto_9-LA1511_S+higa_9 1.0000000
## M248_S+lowga_9-LA1511_S+higa_9 0.9368479
## M248_S+only_9-LA1511_S+higa_9 1.0000000
## LA1511_S+lowaba_9-LA1511_S+iaa_9 0.9960309
## LA1511_S+lowacc_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+iaa_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+iaa_9 0.8790662
## LA1511_S+only_9-LA1511_S+iaa_9 0.9141614
## M058_S+hiaba_9-LA1511_S+iaa_9 0.7038208
## M058_S+hiacc_9-LA1511_S+iaa_9 1.0000000
## M058_S+hicyto_9-LA1511_S+iaa_9 1.0000000
## M058_S+higa_9-LA1511_S+iaa_9 0.1099403
## M058_S+iaa_9-LA1511_S+iaa_9 0.9999993
## M058_S+lowaba_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowacc_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+iaa_9 1.0000000
## M058_S+lowga_9-LA1511_S+iaa_9 0.5054969
## M058_S+only_9-LA1511_S+iaa_9 0.5964766
## M248_S+hiaba_9-LA1511_S+iaa_9 0.1136658
## M248_S+hiacc_9-LA1511_S+iaa_9 1.0000000
## M248_S+hicyto_9-LA1511_S+iaa_9 1.0000000
## M248_S+higa_9-LA1511_S+iaa_9 0.9999174
## M248_S+iaa_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowaba_9-LA1511_S+iaa_9 0.0364368
## M248_S+lowacc_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+iaa_9 1.0000000
## M248_S+lowga_9-LA1511_S+iaa_9 0.0942966
## M248_S+only_9-LA1511_S+iaa_9 0.5657123
## LA1511_S+lowacc_9-LA1511_S+lowaba_9 0.9986282
## LA1511_S+lowcyto_9-LA1511_S+lowaba_9 0.9844609
## LA1511_S+lowga_9-LA1511_S+lowaba_9 1.0000000
## LA1511_S+only_9-LA1511_S+lowaba_9 1.0000000
## M058_S+hiaba_9-LA1511_S+lowaba_9 1.0000000
## M058_S+hiacc_9-LA1511_S+lowaba_9 1.0000000
## M058_S+hicyto_9-LA1511_S+lowaba_9 1.0000000
## M058_S+higa_9-LA1511_S+lowaba_9 0.9944906
## M058_S+iaa_9-LA1511_S+lowaba_9 1.0000000
## M058_S+lowaba_9-LA1511_S+lowaba_9 0.9815458
## M058_S+lowacc_9-LA1511_S+lowaba_9 0.9989781
## M058_S+lowcyto_9-LA1511_S+lowaba_9 0.9513976
## M058_S+lowga_9-LA1511_S+lowaba_9 0.9999995
## M058_S+only_9-LA1511_S+lowaba_9 1.0000000
## M248_S+hiaba_9-LA1511_S+lowaba_9 0.9928793
## M248_S+hiacc_9-LA1511_S+lowaba_9 0.9968060
## M248_S+hicyto_9-LA1511_S+lowaba_9 0.7124987
## M248_S+higa_9-LA1511_S+lowaba_9 1.0000000
## M248_S+iaa_9-LA1511_S+lowaba_9 0.9999961
## M248_S+lowaba_9-LA1511_S+lowaba_9 0.9414197
## M248_S+lowacc_9-LA1511_S+lowaba_9 0.9993608
## M248_S+lowcyto_9-LA1511_S+lowaba_9 0.9999999
## M248_S+lowga_9-LA1511_S+lowaba_9 0.9915097
## M248_S+only_9-LA1511_S+lowaba_9 1.0000000
## LA1511_S+lowcyto_9-LA1511_S+lowacc_9 1.0000000
## LA1511_S+lowga_9-LA1511_S+lowacc_9 0.9476045
## LA1511_S+only_9-LA1511_S+lowacc_9 0.9791863
## M058_S+hiaba_9-LA1511_S+lowacc_9 0.8280076
## M058_S+hiacc_9-LA1511_S+lowacc_9 1.0000000
## M058_S+hicyto_9-LA1511_S+lowacc_9 1.0000000
## M058_S+higa_9-LA1511_S+lowacc_9 0.2451077
## M058_S+iaa_9-LA1511_S+lowacc_9 0.9999997
## M058_S+lowaba_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowacc_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+lowacc_9 1.0000000
## M058_S+lowga_9-LA1511_S+lowacc_9 0.6916847
## M058_S+only_9-LA1511_S+lowacc_9 0.8392006
## M248_S+hiaba_9-LA1511_S+lowacc_9 0.2425788
## M248_S+hiacc_9-LA1511_S+lowacc_9 1.0000000
## M248_S+hicyto_9-LA1511_S+lowacc_9 1.0000000
## M248_S+higa_9-LA1511_S+lowacc_9 0.9999717
## M248_S+iaa_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowaba_9-LA1511_S+lowacc_9 0.1084473
## M248_S+lowacc_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+lowacc_9 1.0000000
## M248_S+lowga_9-LA1511_S+lowacc_9 0.2193197
## M248_S+only_9-LA1511_S+lowacc_9 0.8244673
## LA1511_S+lowga_9-LA1511_S+lowcyto_9 0.7747525
## LA1511_S+only_9-LA1511_S+lowcyto_9 0.8013237
## M058_S+hiaba_9-LA1511_S+lowcyto_9 0.5727701
## M058_S+hiacc_9-LA1511_S+lowcyto_9 0.9999999
## M058_S+hicyto_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+higa_9-LA1511_S+lowcyto_9 0.0647904
## M058_S+iaa_9-LA1511_S+lowcyto_9 0.9999847
## M058_S+lowaba_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowacc_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowcyto_9-LA1511_S+lowcyto_9 1.0000000
## M058_S+lowga_9-LA1511_S+lowcyto_9 0.3703604
## M058_S+only_9-LA1511_S+lowcyto_9 0.4209154
## M248_S+hiaba_9-LA1511_S+lowcyto_9 0.0681442
## M248_S+hiacc_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+hicyto_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+higa_9-LA1511_S+lowcyto_9 0.9992883
## M248_S+iaa_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowaba_9-LA1511_S+lowcyto_9 0.0196238
## M248_S+lowacc_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowcyto_9-LA1511_S+lowcyto_9 1.0000000
## M248_S+lowga_9-LA1511_S+lowcyto_9 0.0547747
## M248_S+only_9-LA1511_S+lowcyto_9 0.3905483
## LA1511_S+only_9-LA1511_S+lowga_9 1.0000000
## M058_S+hiaba_9-LA1511_S+lowga_9 1.0000000
## M058_S+hiacc_9-LA1511_S+lowga_9 0.9997849
## M058_S+hicyto_9-LA1511_S+lowga_9 0.9996641
## M058_S+higa_9-LA1511_S+lowga_9 0.9999820
## M058_S+iaa_9-LA1511_S+lowga_9 0.9999971
## M058_S+lowaba_9-LA1511_S+lowga_9 0.7446321
## M058_S+lowacc_9-LA1511_S+lowga_9 0.9309082
## M058_S+lowcyto_9-LA1511_S+lowga_9 0.6175817
## M058_S+lowga_9-LA1511_S+lowga_9 1.0000000
## M058_S+only_9-LA1511_S+lowga_9 1.0000000
## M248_S+hiaba_9-LA1511_S+lowga_9 0.9999643
## M248_S+hiacc_9-LA1511_S+lowga_9 0.8828171
## M248_S+hicyto_9-LA1511_S+lowga_9 0.2875164
## M248_S+higa_9-LA1511_S+lowga_9 1.0000000
## M248_S+iaa_9-LA1511_S+lowga_9 0.9953860
## M248_S+lowaba_9-LA1511_S+lowga_9 0.9981997
## M248_S+lowacc_9-LA1511_S+lowga_9 0.9492874
## M248_S+lowcyto_9-LA1511_S+lowga_9 0.9992999
## M248_S+lowga_9-LA1511_S+lowga_9 0.9999584
## M248_S+only_9-LA1511_S+lowga_9 1.0000000
## M058_S+hiaba_9-LA1511_S+only_9 0.9999990
## M058_S+hiacc_9-LA1511_S+only_9 0.9999962
## M058_S+hicyto_9-LA1511_S+only_9 0.9999919
## M058_S+higa_9-LA1511_S+only_9 0.9045406
## M058_S+iaa_9-LA1511_S+only_9 1.0000000
## M058_S+lowaba_9-LA1511_S+only_9 0.7521448
## M058_S+lowacc_9-LA1511_S+only_9 0.9579597
## M058_S+lowcyto_9-LA1511_S+only_9 0.5934154
## M058_S+lowga_9-LA1511_S+only_9 0.9999455
## M058_S+only_9-LA1511_S+only_9 1.0000000
## M248_S+hiaba_9-LA1511_S+only_9 0.9028637
## M248_S+hiacc_9-LA1511_S+only_9 0.9117479
## M248_S+hicyto_9-LA1511_S+only_9 0.2434377
## M248_S+higa_9-LA1511_S+only_9 1.0000000
## M248_S+iaa_9-LA1511_S+only_9 0.9993258
## M248_S+lowaba_9-LA1511_S+only_9 0.6067734
## M248_S+lowacc_9-LA1511_S+only_9 0.9751045
## M248_S+lowcyto_9-LA1511_S+only_9 0.9999715
## M248_S+lowga_9-LA1511_S+only_9 0.8732702
## M248_S+only_9-LA1511_S+only_9 1.0000000
## M058_S+hiacc_9-M058_S+hiaba_9 0.9929571
## M058_S+hicyto_9-M058_S+hiaba_9 0.9916059
## M058_S+higa_9-M058_S+hiaba_9 1.0000000
## M058_S+iaa_9-M058_S+hiaba_9 0.9994245
## M058_S+lowaba_9-M058_S+hiaba_9 0.5392499
## M058_S+lowacc_9-M058_S+hiaba_9 0.7858608
## M058_S+lowcyto_9-M058_S+hiaba_9 0.4181401
## M058_S+lowga_9-M058_S+hiaba_9 1.0000000
## M058_S+only_9-M058_S+hiaba_9 1.0000000
## M248_S+hiaba_9-M058_S+hiaba_9 1.0000000
## M248_S+hiacc_9-M058_S+hiaba_9 0.7077357
## M248_S+hicyto_9-M058_S+hiaba_9 0.1706427
## M248_S+higa_9-M058_S+hiaba_9 0.9999869
## M248_S+iaa_9-M058_S+hiaba_9 0.9569156
## M248_S+lowaba_9-M058_S+hiaba_9 0.9999997
## M248_S+lowacc_9-M058_S+hiaba_9 0.8232717
## M248_S+lowcyto_9-M058_S+hiaba_9 0.9863653
## M248_S+lowga_9-M058_S+hiaba_9 1.0000000
## M248_S+only_9-M058_S+hiaba_9 1.0000000
## M058_S+hicyto_9-M058_S+hiacc_9 1.0000000
## M058_S+higa_9-M058_S+hiacc_9 0.5960634
## M058_S+iaa_9-M058_S+hiacc_9 1.0000000
## M058_S+lowaba_9-M058_S+hiacc_9 0.9999999
## M058_S+lowacc_9-M058_S+hiacc_9 1.0000000
## M058_S+lowcyto_9-M058_S+hiacc_9 0.9999976
## M058_S+lowga_9-M058_S+hiacc_9 0.9692203
## M058_S+only_9-M058_S+hiacc_9 0.9969547
## M248_S+hiaba_9-M058_S+hiacc_9 0.5907210
## M248_S+hiacc_9-M058_S+hiacc_9 1.0000000
## M248_S+hicyto_9-M058_S+hiacc_9 0.9976206
## M248_S+higa_9-M058_S+hiacc_9 1.0000000
## M248_S+iaa_9-M058_S+hiacc_9 1.0000000
## M248_S+lowaba_9-M058_S+hiacc_9 0.3193140
## M248_S+lowacc_9-M058_S+hiacc_9 1.0000000
## M248_S+lowcyto_9-M058_S+hiacc_9 1.0000000
## M248_S+lowga_9-M058_S+hiacc_9 0.5522374
## M248_S+only_9-M058_S+hiacc_9 0.9960494
## M058_S+higa_9-M058_S+hicyto_9 0.6234151
## M058_S+iaa_9-M058_S+hicyto_9 1.0000000
## M058_S+lowaba_9-M058_S+hicyto_9 1.0000000
## M058_S+lowacc_9-M058_S+hicyto_9 1.0000000
## M058_S+lowcyto_9-M058_S+hicyto_9 1.0000000
## M058_S+lowga_9-M058_S+hicyto_9 0.9681633
## M058_S+only_9-M058_S+hicyto_9 0.9970086
## M248_S+hiaba_9-M058_S+hicyto_9 0.6146537
## M248_S+hiacc_9-M058_S+hicyto_9 1.0000000
## M248_S+hicyto_9-M058_S+hicyto_9 0.9997372
## M248_S+higa_9-M058_S+hicyto_9 1.0000000
## M248_S+iaa_9-M058_S+hicyto_9 1.0000000
## M248_S+lowaba_9-M058_S+hicyto_9 0.3570475
## M248_S+lowacc_9-M058_S+hicyto_9 1.0000000
## M248_S+lowcyto_9-M058_S+hicyto_9 1.0000000
## M248_S+lowga_9-M058_S+hicyto_9 0.5823236
## M248_S+only_9-M058_S+hicyto_9 0.9962611
## M058_S+iaa_9-M058_S+higa_9 0.8030430
## M058_S+lowaba_9-M058_S+higa_9 0.0511602
## M058_S+lowacc_9-M058_S+higa_9 0.1427248
## M058_S+lowcyto_9-M058_S+higa_9 0.0295793
## M058_S+lowga_9-M058_S+higa_9 1.0000000
## M058_S+only_9-M058_S+higa_9 0.9965089
## M248_S+hiaba_9-M058_S+higa_9 1.0000000
## M248_S+hiacc_9-M058_S+higa_9 0.1026266
## M248_S+hicyto_9-M058_S+higa_9 0.0077203
## M248_S+higa_9-M058_S+higa_9 0.9414197
## M248_S+iaa_9-M058_S+higa_9 0.3695773
## M248_S+lowaba_9-M058_S+higa_9 1.0000000
## M248_S+lowacc_9-M058_S+higa_9 0.1818115
## M248_S+lowcyto_9-M058_S+higa_9 0.5425126
## M248_S+lowga_9-M058_S+higa_9 1.0000000
## M248_S+only_9-M058_S+higa_9 0.9961224
## M058_S+lowaba_9-M058_S+iaa_9 0.9999826
## M058_S+lowacc_9-M058_S+iaa_9 1.0000000
## M058_S+lowcyto_9-M058_S+iaa_9 0.9998268
## M058_S+lowga_9-M058_S+iaa_9 0.9959429
## M058_S+only_9-M058_S+iaa_9 0.9999493
## M248_S+hiaba_9-M058_S+iaa_9 0.7940440
## M248_S+hiacc_9-M058_S+iaa_9 0.9999997
## M248_S+hicyto_9-M058_S+iaa_9 0.9807859
## M248_S+higa_9-M058_S+iaa_9 1.0000000
## M248_S+iaa_9-M058_S+iaa_9 1.0000000
## M248_S+lowaba_9-M058_S+iaa_9 0.5303217
## M248_S+lowacc_9-M058_S+iaa_9 1.0000000
## M248_S+lowcyto_9-M058_S+iaa_9 1.0000000
## M248_S+lowga_9-M058_S+iaa_9 0.7673833
## M248_S+only_9-M058_S+iaa_9 0.9999278
## M058_S+lowacc_9-M058_S+lowaba_9 1.0000000
## M058_S+lowcyto_9-M058_S+lowaba_9 1.0000000
## M058_S+lowga_9-M058_S+lowaba_9 0.3315217
## M058_S+only_9-M058_S+lowaba_9 0.3508915
## M248_S+hiaba_9-M058_S+lowaba_9 0.0547747
## M248_S+hiacc_9-M058_S+lowaba_9 1.0000000
## M248_S+hicyto_9-M058_S+lowaba_9 1.0000000
## M248_S+higa_9-M058_S+lowaba_9 0.9991559
## M248_S+iaa_9-M058_S+lowaba_9 1.0000000
## M248_S+lowaba_9-M058_S+lowaba_9 0.0144220
## M248_S+lowacc_9-M058_S+lowaba_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowaba_9 1.0000000
## M248_S+lowga_9-M058_S+lowaba_9 0.0427981
## M248_S+only_9-M058_S+lowaba_9 0.3200784
## M058_S+lowcyto_9-M058_S+lowacc_9 1.0000000
## M058_S+lowga_9-M058_S+lowacc_9 0.5960634
## M058_S+only_9-M058_S+lowacc_9 0.6921128
## M248_S+hiaba_9-M058_S+lowacc_9 0.1473953
## M248_S+hiacc_9-M058_S+lowacc_9 1.0000000
## M248_S+hicyto_9-M058_S+lowacc_9 0.9999998
## M248_S+higa_9-M058_S+lowacc_9 0.9999916
## M248_S+iaa_9-M058_S+lowacc_9 1.0000000
## M248_S+lowaba_9-M058_S+lowacc_9 0.0482282
## M248_S+lowacc_9-M058_S+lowacc_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowacc_9 1.0000000
## M248_S+lowga_9-M058_S+lowacc_9 0.1229221
## M248_S+only_9-M058_S+lowacc_9 0.6614633
## M058_S+lowga_9-M058_S+lowcyto_9 0.2312005
## M058_S+only_9-M058_S+lowcyto_9 0.2222380
## M248_S+hiaba_9-M058_S+lowcyto_9 0.0323032
## M248_S+hiacc_9-M058_S+lowcyto_9 1.0000000
## M248_S+hicyto_9-M058_S+lowcyto_9 1.0000000
## M248_S+higa_9-M058_S+lowcyto_9 0.9959429
## M248_S+iaa_9-M058_S+lowcyto_9 1.0000000
## M248_S+lowaba_9-M058_S+lowcyto_9 0.0077214
## M248_S+lowacc_9-M058_S+lowcyto_9 1.0000000
## M248_S+lowcyto_9-M058_S+lowcyto_9 0.9999999
## M248_S+lowga_9-M058_S+lowcyto_9 0.0244423
## M248_S+only_9-M058_S+lowcyto_9 0.1979574
## M058_S+only_9-M058_S+lowga_9 1.0000000
## M248_S+hiaba_9-M058_S+lowga_9 1.0000000
## M248_S+hiacc_9-M058_S+lowga_9 0.5012476
## M248_S+hicyto_9-M058_S+lowga_9 0.0775448
## M248_S+higa_9-M058_S+lowga_9 0.9998268
## M248_S+iaa_9-M058_S+lowga_9 0.8742339
## M248_S+lowaba_9-M058_S+lowga_9 0.9999999
## M248_S+lowacc_9-M058_S+lowga_9 0.6546297
## M248_S+lowcyto_9-M058_S+lowga_9 0.9504976
## M248_S+lowga_9-M058_S+lowga_9 1.0000000
## M248_S+only_9-M058_S+lowga_9 1.0000000
## M248_S+hiaba_9-M058_S+only_9 0.9956218
## M248_S+hiacc_9-M058_S+only_9 0.5737402
## M248_S+hicyto_9-M058_S+only_9 0.0663774
## M248_S+higa_9-M058_S+only_9 1.0000000
## M248_S+iaa_9-M058_S+only_9 0.9576491
## M248_S+lowaba_9-M058_S+only_9 0.9268184
## M248_S+lowacc_9-M058_S+only_9 0.7723762
## M248_S+lowcyto_9-M058_S+only_9 0.9928164
## M248_S+lowga_9-M058_S+only_9 0.9937315
## M248_S+only_9-M058_S+only_9 1.0000000
## M248_S+hiacc_9-M248_S+hiaba_9 0.1071971
## M248_S+hicyto_9-M248_S+hiaba_9 0.0085856
## M248_S+higa_9-M248_S+hiaba_9 0.9346576
## M248_S+iaa_9-M248_S+hiaba_9 0.3703604
## M248_S+lowaba_9-M248_S+hiaba_9 1.0000000
## M248_S+lowacc_9-M248_S+hiaba_9 0.1850597
## M248_S+lowcyto_9-M248_S+hiaba_9 0.5371423
## M248_S+lowga_9-M248_S+hiaba_9 1.0000000
## M248_S+only_9-M248_S+hiaba_9 0.9951982
## M248_S+hicyto_9-M248_S+hiacc_9 1.0000000
## M248_S+higa_9-M248_S+hiacc_9 0.9999488
## M248_S+iaa_9-M248_S+hiacc_9 1.0000000
## M248_S+lowaba_9-M248_S+hiacc_9 0.0324908
## M248_S+lowacc_9-M248_S+hiacc_9 1.0000000
## M248_S+lowcyto_9-M248_S+hiacc_9 1.0000000
## M248_S+lowga_9-M248_S+hiacc_9 0.0874662
## M248_S+only_9-M248_S+hiacc_9 0.5401518
## M248_S+higa_9-M248_S+hicyto_9 0.9110446
## M248_S+iaa_9-M248_S+hicyto_9 0.9998882
## M248_S+lowaba_9-M248_S+hicyto_9 0.0018888
## M248_S+lowacc_9-M248_S+hicyto_9 0.9999999
## M248_S+lowcyto_9-M248_S+hicyto_9 0.9996131
## M248_S+lowga_9-M248_S+hicyto_9 0.0063027
## M248_S+only_9-M248_S+hicyto_9 0.0577167
## M248_S+iaa_9-M248_S+higa_9 1.0000000
## M248_S+lowaba_9-M248_S+higa_9 0.7611749
## M248_S+lowacc_9-M248_S+higa_9 0.9999953
## M248_S+lowcyto_9-M248_S+higa_9 1.0000000
## M248_S+lowga_9-M248_S+higa_9 0.9238383
## M248_S+only_9-M248_S+higa_9 0.9999999
## M248_S+lowaba_9-M248_S+iaa_9 0.1610242
## M248_S+lowacc_9-M248_S+iaa_9 1.0000000
## M248_S+lowcyto_9-M248_S+iaa_9 1.0000000
## M248_S+lowga_9-M248_S+iaa_9 0.3315217
## M248_S+only_9-M248_S+iaa_9 0.9492626
## M248_S+lowacc_9-M248_S+lowaba_9 0.0668063
## M248_S+lowcyto_9-M248_S+lowaba_9 0.2827454
## M248_S+lowga_9-M248_S+lowaba_9 1.0000000
## M248_S+only_9-M248_S+lowaba_9 0.9206677
## M248_S+lowcyto_9-M248_S+lowacc_9 1.0000000
## M248_S+lowga_9-M248_S+lowacc_9 0.1585448
## M248_S+only_9-M248_S+lowacc_9 0.7477555
## M248_S+lowga_9-M248_S+lowcyto_9 0.5000157
## M248_S+only_9-M248_S+lowcyto_9 0.9910487
## M248_S+only_9-M248_S+lowga_9 0.9930560P8 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P8)
stat.test## LA1511_S+hiacc_9 LA1511_S+hicyto_9 LA1511_S+higa_9 LA1511_S+iaa_9
## "abcd" "a" "abcd" "abc"
## LA1511_S+lowaba_9 LA1511_S+lowacc_9 LA1511_S+lowcyto_9 LA1511_S+lowga_9
## "abcd" "abcd" "abc" "abcd"
## LA1511_S+only_9 M058_S+hiaba_9 M058_S+hiacc_9 M058_S+hicyto_9
## "abcd" "abcd" "abcd" "abcd"
## M058_S+higa_9 M058_S+iaa_9 M058_S+lowaba_9 M058_S+lowacc_9
## "bcd" "abcd" "ac" "abc"
## M058_S+lowcyto_9 M058_S+lowga_9 M058_S+only_9 M248_S+hiaba_9
## "a" "abcd" "abcd" "bcd"
## M248_S+hiacc_9 M248_S+hicyto_9 M248_S+higa_9 M248_S+iaa_9
## "abc" "a" "abcd" "abcd"
## M248_S+lowaba_9 M248_S+lowacc_9 M248_S+lowcyto_9 M248_S+lowga_9
## "d" "abcd" "abcd" "bd"
## M248_S+only_9 LA1511_S+hiaba_9
## "abcd" "abcd"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "S+hiacc"test$info[[1]][3]## [1] "9"test$Accession <- "none"
test$All.condition<- "none"
test$Day<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
test$Day[i] <- test$info[[i]][3]
}
test2 <- test[,c(5:7,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
all_data2all_data2$All.condition <- factor(all_data2$All.condition, levels = c("S+only", "S+iaa", "S+lowacc", "S+hiacc", "S+lowaba", "S+hiaba", "S+lowga", "S+higa", "S+lowcyto", "S+hicyto"))
alpha_all <- ggplot(data = all_data2, mapping = aes(x = All.condition, y = Alpha, colour = All.condition))
alpha_all <- alpha_all + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
alpha_all <- alpha_all + facet_grid(~ Accession, scales = "free_y")
alpha_all <- alpha_all + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
alpha_all <- alpha_all + scale_color_manual(values = c("blueviolet","cyan", "pink", "pink4", "green","green4", "magenta", "magenta4", "red1", "red4"))
alpha_all <- alpha_all + ylab("Alpha") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 1.2)
alpha_all <- alpha_all + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
alpha_all <- alpha_all + rremove("legend")
alpha_all
#Now plot pareto components for the ABA treatment for 3 accessions.
list.files(pattern=".csv")## [1] "ABA-only.csv"
## [2] "ACC-only-d5excluded.csv"
## [3] "ACC-only.csv"
## [4] "cyto-only.csv"
## [5] "GA-only-d5excluded.csv"
## [6] "GA-only.csv"
## [7] "IAA-only-d5excluded.csv"
## [8] "IAA-only.csv"
## [9] "point_similarity_maryamModified.csv"
## [10] "point_similarity_maryamModified_control_Removed.csv"ABA_data <- read.csv("ABA-only.csv")
ABA_dataABA_data$All.condition<-paste(ABA_data$Condition1,ABA_data$Condition2, sep="+")
ABA_dataABA_data$All.ID2<-paste(ABA_data$Accession,ABA_data$All.condition,sep="_")
ABA_datalibrary(ggplot2)
library(ggpubr)
library(multcompView)
aov(Distance.squared ~ All.ID2, data = ABA_data)## Call:
## aov(formula = Distance.squared ~ All.ID2, data = ABA_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 45671.89 181896.99
## Deg. of Freedom 17 145
##
## Residual standard error: 35.41839
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Distance.squared ~ All.ID2, data = ABA_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Distance.squared ~ All.ID2, data = ABA_data)
##
## $All.ID2
## diff lwr upr p adj
## LA1511_C+lowaba-LA1511_C+hiaba -0.26151560 -59.950461 59.427430 1.0000000
## LA1511_C+noaba-LA1511_C+hiaba 6.52633407 -51.291017 64.343685 1.0000000
## LA1511_S+hiaba-LA1511_C+hiaba -1.91483043 -66.895924 63.066263 1.0000000
## LA1511_S+lowaba-LA1511_C+hiaba -1.57585480 -57.851132 54.699423 1.0000000
## LA1511_S+noaba-LA1511_C+hiaba 0.07822980 -56.197048 56.353507 1.0000000
## M058_C+hiaba-LA1511_C+hiaba -1.65866050 -57.933938 54.616617 1.0000000
## M058_C+lowaba-LA1511_C+hiaba 1.87705554 -60.135280 63.889391 1.0000000
## M058_C+noaba-LA1511_C+hiaba 4.04416680 -52.231111 60.319444 1.0000000
## M058_S+hiaba-LA1511_C+hiaba -1.55514547 -61.244091 58.133800 1.0000000
## M058_S+lowaba-LA1511_C+hiaba -1.53113350 -57.806411 54.744144 1.0000000
## M058_S+noaba-LA1511_C+hiaba 0.48115600 -55.794121 56.756433 1.0000000
## M248_C+hiaba-LA1511_C+hiaba 3.86996010 -52.405317 60.145238 1.0000000
## M248_C+lowaba-LA1511_C+hiaba 5.40799497 -56.604340 67.420330 1.0000000
## M248_C+noaba-LA1511_C+hiaba 69.81975270 13.544475 126.095030 0.0025968
## M248_S+hiaba-LA1511_C+hiaba 0.95189651 -56.865455 58.769248 1.0000000
## M248_S+lowaba-LA1511_C+hiaba 6.34579000 -49.929487 62.621067 1.0000000
## M248_S+noaba-LA1511_C+hiaba 14.33968729 -43.477664 72.157039 0.9999880
## LA1511_C+noaba-LA1511_C+lowaba 6.78784967 -54.357138 67.932837 1.0000000
## LA1511_S+hiaba-LA1511_C+lowaba -1.65331483 -69.612169 66.305539 1.0000000
## LA1511_S+lowaba-LA1511_C+lowaba -1.31433920 -61.003285 58.374606 1.0000000
## LA1511_S+noaba-LA1511_C+lowaba 0.33974540 -59.349200 60.028691 1.0000000
## M058_C+hiaba-LA1511_C+lowaba -1.39714490 -61.086090 58.291801 1.0000000
## M058_C+lowaba-LA1511_C+lowaba 2.13857114 -62.987408 67.264550 1.0000000
## M058_C+noaba-LA1511_C+lowaba 4.30568240 -55.383263 63.994628 1.0000000
## M058_S+hiaba-LA1511_C+lowaba -1.29362987 -64.211303 61.624043 1.0000000
## M058_S+lowaba-LA1511_C+lowaba -1.26961790 -60.958563 58.419328 1.0000000
## M058_S+noaba-LA1511_C+lowaba 0.74267160 -58.946274 60.431617 1.0000000
## M248_C+hiaba-LA1511_C+lowaba 4.13147570 -55.557470 63.820421 1.0000000
## M248_C+lowaba-LA1511_C+lowaba 5.66951057 -59.456468 70.795489 1.0000000
## M248_C+noaba-LA1511_C+lowaba 70.08126830 10.392323 129.770214 0.0063252
## M248_S+hiaba-LA1511_C+lowaba 1.21341211 -59.931575 62.358399 1.0000000
## M248_S+lowaba-LA1511_C+lowaba 6.60730560 -53.081640 66.296251 1.0000000
## M248_S+noaba-LA1511_C+lowaba 14.60120289 -46.543784 75.746190 0.9999931
## LA1511_S+hiaba-LA1511_C+noaba -8.44116450 -74.762215 57.879886 1.0000000
## LA1511_S+lowaba-LA1511_C+noaba -8.10218887 -65.919540 49.715163 1.0000000
## LA1511_S+noaba-LA1511_C+noaba -6.44810427 -64.265456 51.369247 1.0000000
## M058_C+hiaba-LA1511_C+noaba -8.18499457 -66.002346 49.632357 1.0000000
## M058_C+lowaba-LA1511_C+noaba -4.64927852 -68.064332 58.765775 1.0000000
## M058_C+noaba-LA1511_C+noaba -2.48216727 -60.299519 55.335184 1.0000000
## M058_S+hiaba-LA1511_C+noaba -8.08147954 -69.226467 53.063508 1.0000000
## M058_S+lowaba-LA1511_C+noaba -8.05746757 -65.874819 49.759884 1.0000000
## M058_S+noaba-LA1511_C+noaba -6.04517807 -63.862529 51.772173 1.0000000
## M248_C+hiaba-LA1511_C+noaba -2.65637397 -60.473725 55.160977 1.0000000
## M248_C+lowaba-LA1511_C+noaba -1.11833910 -64.533393 62.296714 1.0000000
## M248_C+noaba-LA1511_C+noaba 63.29341863 5.476067 121.110770 0.0170739
## M248_S+hiaba-LA1511_C+noaba -5.57443756 -64.893788 53.744913 1.0000000
## M248_S+lowaba-LA1511_C+noaba -0.18054407 -57.997895 57.636807 1.0000000
## M248_S+noaba-LA1511_C+noaba 7.81335322 -51.505998 67.132704 1.0000000
## LA1511_S+lowaba-LA1511_S+hiaba 0.33897563 -64.642118 65.320069 1.0000000
## LA1511_S+noaba-LA1511_S+hiaba 1.99306023 -62.988033 66.974153 1.0000000
## M058_C+hiaba-LA1511_S+hiaba 0.25616993 -64.724923 65.237263 1.0000000
## M058_C+lowaba-LA1511_S+hiaba 3.79188598 -66.216438 73.800210 1.0000000
## M058_C+noaba-LA1511_S+hiaba 5.95899723 -59.022096 70.940090 1.0000000
## M058_S+hiaba-LA1511_S+hiaba 0.35968496 -67.599169 68.318539 1.0000000
## M058_S+lowaba-LA1511_S+hiaba 0.38369693 -64.597396 65.364790 1.0000000
## M058_S+noaba-LA1511_S+hiaba 2.39598643 -62.585107 67.377080 1.0000000
## M248_C+hiaba-LA1511_S+hiaba 5.78479053 -59.196303 70.765884 1.0000000
## M248_C+lowaba-LA1511_S+hiaba 7.32282540 -62.685498 77.331149 1.0000000
## M248_C+noaba-LA1511_S+hiaba 71.73458313 6.753490 136.715676 0.0152773
## M248_S+hiaba-LA1511_S+hiaba 2.86672694 -63.454324 69.187777 1.0000000
## M248_S+lowaba-LA1511_S+hiaba 8.26062043 -56.720473 73.241714 1.0000000
## M248_S+noaba-LA1511_S+hiaba 16.25451772 -50.066533 82.575568 0.9999899
## LA1511_S+noaba-LA1511_S+lowaba 1.65408460 -54.621193 57.929362 1.0000000
## M058_C+hiaba-LA1511_S+lowaba -0.08280570 -56.358083 56.192472 1.0000000
## M058_C+lowaba-LA1511_S+lowaba 3.45291034 -58.559425 65.465246 1.0000000
## M058_C+noaba-LA1511_S+lowaba 5.62002160 -50.655256 61.895299 1.0000000
## M058_S+hiaba-LA1511_S+lowaba 0.02070933 -59.668236 59.709655 1.0000000
## M058_S+lowaba-LA1511_S+lowaba 0.04472130 -56.230556 56.319999 1.0000000
## M058_S+noaba-LA1511_S+lowaba 2.05701080 -54.218267 58.332288 1.0000000
## M248_C+hiaba-LA1511_S+lowaba 5.44581490 -50.829463 61.721092 1.0000000
## M248_C+lowaba-LA1511_S+lowaba 6.98384977 -55.028486 68.996185 1.0000000
## M248_C+noaba-LA1511_S+lowaba 71.39560750 15.120330 127.670885 0.0017601
## M248_S+hiaba-LA1511_S+lowaba 2.52775131 -55.289600 60.345103 1.0000000
## M248_S+lowaba-LA1511_S+lowaba 7.92164480 -48.353633 64.196922 1.0000000
## M248_S+noaba-LA1511_S+lowaba 15.91554209 -41.901809 73.732893 0.9999472
## M058_C+hiaba-LA1511_S+noaba -1.73689030 -58.012168 54.538387 1.0000000
## M058_C+lowaba-LA1511_S+noaba 1.79882574 -60.213510 63.811161 1.0000000
## M058_C+noaba-LA1511_S+noaba 3.96593700 -52.309340 60.241214 1.0000000
## M058_S+hiaba-LA1511_S+noaba -1.63337527 -61.322321 58.055570 1.0000000
## M058_S+lowaba-LA1511_S+noaba -1.60936330 -57.884641 54.665914 1.0000000
## M058_S+noaba-LA1511_S+noaba 0.40292620 -55.872351 56.678204 1.0000000
## M248_C+hiaba-LA1511_S+noaba 3.79173030 -52.483547 60.067008 1.0000000
## M248_C+lowaba-LA1511_S+noaba 5.32976517 -56.682570 67.342101 1.0000000
## M248_C+noaba-LA1511_S+noaba 69.74152290 13.466245 126.016800 0.0026469
## M248_S+hiaba-LA1511_S+noaba 0.87366671 -56.943685 58.691018 1.0000000
## M248_S+lowaba-LA1511_S+noaba 6.26756020 -50.007717 62.542838 1.0000000
## M248_S+noaba-LA1511_S+noaba 14.26145749 -43.555894 72.078809 0.9999889
## M058_C+lowaba-M058_C+hiaba 3.53571604 -58.476619 65.548051 1.0000000
## M058_C+noaba-M058_C+hiaba 5.70282730 -50.572450 61.978105 1.0000000
## M058_S+hiaba-M058_C+hiaba 0.10351502 -59.585430 59.792460 1.0000000
## M058_S+lowaba-M058_C+hiaba 0.12752700 -56.147750 56.402804 1.0000000
## M058_S+noaba-M058_C+hiaba 2.13981650 -54.135461 58.415094 1.0000000
## M248_C+hiaba-M058_C+hiaba 5.52862060 -50.746657 61.803898 1.0000000
## M248_C+lowaba-M058_C+hiaba 7.06665547 -54.945680 69.078991 1.0000000
## M248_C+noaba-M058_C+hiaba 71.47841320 15.203136 127.753691 0.0017241
## M248_S+hiaba-M058_C+hiaba 2.61055701 -55.206794 60.427908 1.0000000
## M248_S+lowaba-M058_C+hiaba 8.00445050 -48.270827 64.279728 1.0000000
## M248_S+noaba-M058_C+hiaba 15.99834779 -41.819004 73.815699 0.9999432
## M058_C+noaba-M058_C+lowaba 2.16711126 -59.845224 64.179447 1.0000000
## M058_S+hiaba-M058_C+lowaba -3.43220102 -68.558180 61.693778 1.0000000
## M058_S+lowaba-M058_C+lowaba -3.40818904 -65.420524 58.604146 1.0000000
## M058_S+noaba-M058_C+lowaba -1.39589954 -63.408235 60.616436 1.0000000
## M248_C+hiaba-M058_C+lowaba 1.99290456 -60.019431 64.005240 1.0000000
## M248_C+lowaba-M058_C+lowaba 3.53093943 -63.730882 70.792761 1.0000000
## M248_C+noaba-M058_C+lowaba 67.94269716 5.930362 129.955033 0.0168866
## M248_S+hiaba-M058_C+lowaba -0.92515903 -64.340213 62.489895 1.0000000
## M248_S+lowaba-M058_C+lowaba 4.46873446 -57.543601 66.481070 1.0000000
## M248_S+noaba-M058_C+lowaba 12.46263175 -50.952422 75.877685 0.9999996
## M058_S+hiaba-M058_C+noaba -5.59931227 -65.288258 54.089633 1.0000000
## M058_S+lowaba-M058_C+noaba -5.57530030 -61.850578 50.699977 1.0000000
## M058_S+noaba-M058_C+noaba -3.56301080 -59.838288 52.712267 1.0000000
## M248_C+hiaba-M058_C+noaba -0.17420670 -56.449484 56.101071 1.0000000
## M248_C+lowaba-M058_C+noaba 1.36382817 -60.648507 63.376164 1.0000000
## M248_C+noaba-M058_C+noaba 65.77558590 9.500308 122.050863 0.0067740
## M248_S+hiaba-M058_C+noaba -3.09227029 -60.909622 54.725081 1.0000000
## M248_S+lowaba-M058_C+noaba 2.30162320 -53.973654 58.576901 1.0000000
## M248_S+noaba-M058_C+noaba 10.29552049 -47.521831 68.112872 0.9999999
## M058_S+lowaba-M058_S+hiaba 0.02401197 -59.664933 59.712957 1.0000000
## M058_S+noaba-M058_S+hiaba 2.03630147 -57.652644 61.725247 1.0000000
## M248_C+hiaba-M058_S+hiaba 5.42510557 -54.263840 65.114051 1.0000000
## M248_C+lowaba-M058_S+hiaba 6.96314045 -58.162838 72.089119 1.0000000
## M248_C+noaba-M058_S+hiaba 71.37489817 11.685953 131.063844 0.0047598
## M248_S+hiaba-M058_S+hiaba 2.50704199 -58.637945 63.652029 1.0000000
## M248_S+lowaba-M058_S+hiaba 7.90093547 -51.788010 67.589881 1.0000000
## M248_S+noaba-M058_S+hiaba 15.89483276 -45.250155 77.039820 0.9999764
## M058_S+noaba-M058_S+lowaba 2.01228950 -54.262988 58.287567 1.0000000
## M248_C+hiaba-M058_S+lowaba 5.40109360 -50.874184 61.676371 1.0000000
## M248_C+lowaba-M058_S+lowaba 6.93912847 -55.073207 68.951464 1.0000000
## M248_C+noaba-M058_S+lowaba 71.35088620 15.075609 127.626164 0.0017799
## M248_S+hiaba-M058_S+lowaba 2.48303001 -55.334321 60.300381 1.0000000
## M248_S+lowaba-M058_S+lowaba 7.87692350 -48.398354 64.152201 1.0000000
## M248_S+noaba-M058_S+lowaba 15.87082079 -41.946531 73.688172 0.9999492
## M248_C+hiaba-M058_S+noaba 3.38880410 -52.886473 59.664082 1.0000000
## M248_C+lowaba-M058_S+noaba 4.92683897 -57.085496 66.939174 1.0000000
## M248_C+noaba-M058_S+noaba 69.33859670 13.063319 125.613874 0.0029194
## M248_S+hiaba-M058_S+noaba 0.47074051 -57.346611 58.288092 1.0000000
## M248_S+lowaba-M058_S+noaba 5.86463400 -50.410643 62.139911 1.0000000
## M248_S+noaba-M058_S+noaba 13.85853129 -43.958820 71.675883 0.9999927
## M248_C+lowaba-M248_C+hiaba 1.53803487 -60.474301 63.550370 1.0000000
## M248_C+noaba-M248_C+hiaba 65.94979260 9.674515 122.225070 0.0065079
## M248_S+hiaba-M248_C+hiaba -2.91806359 -60.735415 54.899288 1.0000000
## M248_S+lowaba-M248_C+hiaba 2.47582990 -53.799448 58.751107 1.0000000
## M248_S+noaba-M248_C+hiaba 10.46972719 -47.347624 68.287079 0.9999999
## M248_C+noaba-M248_C+lowaba 64.41175773 2.399422 126.424093 0.0327393
## M248_S+hiaba-M248_C+lowaba -4.45609846 -67.871152 58.958955 1.0000000
## M248_S+lowaba-M248_C+lowaba 0.93779503 -61.074540 62.950130 1.0000000
## M248_S+noaba-M248_C+lowaba 8.93169232 -54.483361 72.346746 1.0000000
## M248_S+hiaba-M248_C+noaba -68.86785619 -126.685208 -11.050505 0.0050617
## M248_S+lowaba-M248_C+noaba -63.47396270 -119.749240 -7.198685 0.0113797
## M248_S+noaba-M248_C+noaba -55.48006541 -113.297417 2.337286 0.0759350
## M248_S+lowaba-M248_S+hiaba 5.39389349 -52.423458 63.211245 1.0000000
## M248_S+noaba-M248_S+hiaba 13.38779078 -45.931560 72.707142 0.9999970
## M248_S+noaba-M248_S+lowaba 7.99389729 -49.823454 65.811249 1.0000000P7 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P7)
stat.test## LA1511_C+lowaba LA1511_C+noaba LA1511_S+hiaba LA1511_S+lowaba LA1511_S+noaba
## "a" "a" "a" "a" "a"
## M058_C+hiaba M058_C+lowaba M058_C+noaba M058_S+hiaba M058_S+lowaba
## "a" "a" "a" "a" "a"
## M058_S+noaba M248_C+hiaba M248_C+lowaba M248_C+noaba M248_S+hiaba
## "a" "a" "a" "b" "a"
## M248_S+lowaba M248_S+noaba LA1511_C+hiaba
## "a" "ab" "a"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowaba"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
ABA_dataABA_data$All.condition <- factor(ABA_data$All.condition, levels = c("C+noaba", "C+lowaba", "C+hiaba", "S+noaba", "S+lowaba", "S+hiaba"))
ABA_data2 <- subset(ABA_data, ABA_data$Distance.squared < 80)
distance_ABA <- ggplot(data = ABA_data2, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_ABA <- distance_ABA + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_ABA <- distance_ABA + facet_grid(~ Accession, scales = "free_y")
distance_ABA <- distance_ABA + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_ABA <- distance_ABA + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
distance_ABA <- distance_ABA + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 70)
distance_ABA <- distance_ABA + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_ABA <- distance_ABA + rremove("legend")
distance_ABA
aov(Alpha ~ All.ID2, data = ABA_data)## Call:
## aov(formula = Alpha ~ All.ID2, data = ABA_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 3.066946 7.320432
## Deg. of Freedom 17 145
##
## Residual standard error: 0.2246903
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Alpha ~ All.ID2, data = ABA_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Alpha ~ All.ID2, data = ABA_data)
##
## $All.ID2
## diff lwr upr
## LA1511_C+lowaba-LA1511_C+hiaba -0.108750000 -0.487410073 0.269910073
## LA1511_C+noaba-LA1511_C+hiaba -0.084444444 -0.451231331 0.282342442
## LA1511_S+hiaba-LA1511_C+hiaba -0.101666667 -0.513899540 0.310566206
## LA1511_S+lowaba-LA1511_C+hiaba -0.021000000 -0.378004140 0.336004140
## LA1511_S+noaba-LA1511_C+hiaba -0.105000000 -0.462004140 0.252004140
## M058_C+hiaba-LA1511_C+hiaba 0.274000000 -0.083004140 0.631004140
## M058_C+lowaba-LA1511_C+hiaba 0.057142857 -0.336256545 0.450542259
## M058_C+noaba-LA1511_C+hiaba 0.080000000 -0.277004140 0.437004140
## M058_S+hiaba-LA1511_C+hiaba -0.133750000 -0.512410073 0.244910073
## M058_S+lowaba-LA1511_C+hiaba 0.198000000 -0.159004140 0.555004140
## M058_S+noaba-LA1511_C+hiaba -0.112000000 -0.469004140 0.245004140
## M248_C+hiaba-LA1511_C+hiaba -0.098000000 -0.455004140 0.259004140
## M248_C+lowaba-LA1511_C+hiaba -0.140000000 -0.533399402 0.253399402
## M248_C+noaba-LA1511_C+hiaba 0.060000000 -0.297004140 0.417004140
## M248_S+hiaba-LA1511_C+hiaba -0.231111111 -0.597897998 0.135675776
## M248_S+lowaba-LA1511_C+hiaba -0.262000000 -0.619004140 0.095004140
## M248_S+noaba-LA1511_C+hiaba -0.083333333 -0.450120220 0.283453553
## LA1511_C+noaba-LA1511_C+lowaba 0.024305556 -0.363591486 0.412202597
## LA1511_S+hiaba-LA1511_C+lowaba 0.007083333 -0.424040125 0.438206791
## LA1511_S+lowaba-LA1511_C+lowaba 0.087750000 -0.290910073 0.466410073
## LA1511_S+noaba-LA1511_C+lowaba 0.003750000 -0.374910073 0.382410073
## M058_C+hiaba-LA1511_C+lowaba 0.382750000 0.004089927 0.761410073
## M058_C+lowaba-LA1511_C+lowaba 0.165892857 -0.247259154 0.579044868
## M058_C+noaba-LA1511_C+lowaba 0.188750000 -0.189910073 0.567410073
## M058_S+hiaba-LA1511_C+lowaba -0.025000000 -0.424142763 0.374142763
## M058_S+lowaba-LA1511_C+lowaba 0.306750000 -0.071910073 0.685410073
## M058_S+noaba-LA1511_C+lowaba -0.003250000 -0.381910073 0.375410073
## M248_C+hiaba-LA1511_C+lowaba 0.010750000 -0.367910073 0.389410073
## M248_C+lowaba-LA1511_C+lowaba -0.031250000 -0.444402011 0.381902011
## M248_C+noaba-LA1511_C+lowaba 0.168750000 -0.209910073 0.547410073
## M248_S+hiaba-LA1511_C+lowaba -0.122361111 -0.510258153 0.265535930
## M248_S+lowaba-LA1511_C+lowaba -0.153250000 -0.531910073 0.225410073
## M248_S+noaba-LA1511_C+lowaba 0.025416667 -0.362480375 0.413313708
## LA1511_S+hiaba-LA1511_C+noaba -0.017222222 -0.437955636 0.403511192
## LA1511_S+lowaba-LA1511_C+noaba 0.063444444 -0.303342442 0.430231331
## LA1511_S+noaba-LA1511_C+noaba -0.020555556 -0.387342442 0.346231331
## M058_C+hiaba-LA1511_C+noaba 0.358444444 -0.008342442 0.725231331
## M058_C+lowaba-LA1511_C+noaba 0.141587302 -0.260710789 0.543885392
## M058_C+noaba-LA1511_C+noaba 0.164444444 -0.202342442 0.531231331
## M058_S+hiaba-LA1511_C+noaba -0.049305556 -0.437202597 0.338591486
## M058_S+lowaba-LA1511_C+noaba 0.282444444 -0.084342442 0.649231331
## M058_S+noaba-LA1511_C+noaba -0.027555556 -0.394342442 0.339231331
## M248_C+hiaba-LA1511_C+noaba -0.013555556 -0.380342442 0.353231331
## M248_C+lowaba-LA1511_C+noaba -0.055555556 -0.457853646 0.346742535
## M248_C+noaba-LA1511_C+noaba 0.144444444 -0.222342442 0.511231331
## M248_S+hiaba-LA1511_C+noaba -0.146666667 -0.522982072 0.229648739
## M248_S+lowaba-LA1511_C+noaba -0.177555556 -0.544342442 0.189231331
## M248_S+noaba-LA1511_C+noaba 0.001111111 -0.375204295 0.377426517
## LA1511_S+lowaba-LA1511_S+hiaba 0.080666667 -0.331566206 0.492899540
## LA1511_S+noaba-LA1511_S+hiaba -0.003333333 -0.415566206 0.408899540
## M058_C+hiaba-LA1511_S+hiaba 0.375666667 -0.036566206 0.787899540
## M058_C+lowaba-LA1511_S+hiaba 0.158809524 -0.285315543 0.602934591
## M058_C+noaba-LA1511_S+hiaba 0.181666667 -0.230566206 0.593899540
## M058_S+hiaba-LA1511_S+hiaba -0.032083333 -0.463206791 0.399040125
## M058_S+lowaba-LA1511_S+hiaba 0.299666667 -0.112566206 0.711899540
## M058_S+noaba-LA1511_S+hiaba -0.010333333 -0.422566206 0.401899540
## M248_C+hiaba-LA1511_S+hiaba 0.003666667 -0.408566206 0.415899540
## M248_C+lowaba-LA1511_S+hiaba -0.038333333 -0.482458400 0.405791733
## M248_C+noaba-LA1511_S+hiaba 0.161666667 -0.250566206 0.573899540
## M248_S+hiaba-LA1511_S+hiaba -0.129444444 -0.550177858 0.291288970
## M248_S+lowaba-LA1511_S+hiaba -0.160333333 -0.572566206 0.251899540
## M248_S+noaba-LA1511_S+hiaba 0.018333333 -0.402400081 0.439066747
## LA1511_S+noaba-LA1511_S+lowaba -0.084000000 -0.441004140 0.273004140
## M058_C+hiaba-LA1511_S+lowaba 0.295000000 -0.062004140 0.652004140
## M058_C+lowaba-LA1511_S+lowaba 0.078142857 -0.315256545 0.471542259
## M058_C+noaba-LA1511_S+lowaba 0.101000000 -0.256004140 0.458004140
## M058_S+hiaba-LA1511_S+lowaba -0.112750000 -0.491410073 0.265910073
## M058_S+lowaba-LA1511_S+lowaba 0.219000000 -0.138004140 0.576004140
## M058_S+noaba-LA1511_S+lowaba -0.091000000 -0.448004140 0.266004140
## M248_C+hiaba-LA1511_S+lowaba -0.077000000 -0.434004140 0.280004140
## M248_C+lowaba-LA1511_S+lowaba -0.119000000 -0.512399402 0.274399402
## M248_C+noaba-LA1511_S+lowaba 0.081000000 -0.276004140 0.438004140
## M248_S+hiaba-LA1511_S+lowaba -0.210111111 -0.576897998 0.156675776
## M248_S+lowaba-LA1511_S+lowaba -0.241000000 -0.598004140 0.116004140
## M248_S+noaba-LA1511_S+lowaba -0.062333333 -0.429120220 0.304453553
## M058_C+hiaba-LA1511_S+noaba 0.379000000 0.021995860 0.736004140
## M058_C+lowaba-LA1511_S+noaba 0.162142857 -0.231256545 0.555542259
## M058_C+noaba-LA1511_S+noaba 0.185000000 -0.172004140 0.542004140
## M058_S+hiaba-LA1511_S+noaba -0.028750000 -0.407410073 0.349910073
## M058_S+lowaba-LA1511_S+noaba 0.303000000 -0.054004140 0.660004140
## M058_S+noaba-LA1511_S+noaba -0.007000000 -0.364004140 0.350004140
## M248_C+hiaba-LA1511_S+noaba 0.007000000 -0.350004140 0.364004140
## M248_C+lowaba-LA1511_S+noaba -0.035000000 -0.428399402 0.358399402
## M248_C+noaba-LA1511_S+noaba 0.165000000 -0.192004140 0.522004140
## M248_S+hiaba-LA1511_S+noaba -0.126111111 -0.492897998 0.240675776
## M248_S+lowaba-LA1511_S+noaba -0.157000000 -0.514004140 0.200004140
## M248_S+noaba-LA1511_S+noaba 0.021666667 -0.345120220 0.388453553
## M058_C+lowaba-M058_C+hiaba -0.216857143 -0.610256545 0.176542259
## M058_C+noaba-M058_C+hiaba -0.194000000 -0.551004140 0.163004140
## M058_S+hiaba-M058_C+hiaba -0.407750000 -0.786410073 -0.029089927
## M058_S+lowaba-M058_C+hiaba -0.076000000 -0.433004140 0.281004140
## M058_S+noaba-M058_C+hiaba -0.386000000 -0.743004140 -0.028995860
## M248_C+hiaba-M058_C+hiaba -0.372000000 -0.729004140 -0.014995860
## M248_C+lowaba-M058_C+hiaba -0.414000000 -0.807399402 -0.020600598
## M248_C+noaba-M058_C+hiaba -0.214000000 -0.571004140 0.143004140
## M248_S+hiaba-M058_C+hiaba -0.505111111 -0.871897998 -0.138324224
## M248_S+lowaba-M058_C+hiaba -0.536000000 -0.893004140 -0.178995860
## M248_S+noaba-M058_C+hiaba -0.357333333 -0.724120220 0.009453553
## M058_C+noaba-M058_C+lowaba 0.022857143 -0.370542259 0.416256545
## M058_S+hiaba-M058_C+lowaba -0.190892857 -0.604044868 0.222259154
## M058_S+lowaba-M058_C+lowaba 0.140857143 -0.252542259 0.534256545
## M058_S+noaba-M058_C+lowaba -0.169142857 -0.562542259 0.224256545
## M248_C+hiaba-M058_C+lowaba -0.155142857 -0.548542259 0.238256545
## M248_C+lowaba-M058_C+lowaba -0.197142857 -0.623844419 0.229558705
## M248_C+noaba-M058_C+lowaba 0.002857143 -0.390542259 0.396256545
## M248_S+hiaba-M058_C+lowaba -0.288253968 -0.690552059 0.114044122
## M248_S+lowaba-M058_C+lowaba -0.319142857 -0.712542259 0.074256545
## M248_S+noaba-M058_C+lowaba -0.140476190 -0.542774281 0.261821900
## M058_S+hiaba-M058_C+noaba -0.213750000 -0.592410073 0.164910073
## M058_S+lowaba-M058_C+noaba 0.118000000 -0.239004140 0.475004140
## M058_S+noaba-M058_C+noaba -0.192000000 -0.549004140 0.165004140
## M248_C+hiaba-M058_C+noaba -0.178000000 -0.535004140 0.179004140
## M248_C+lowaba-M058_C+noaba -0.220000000 -0.613399402 0.173399402
## M248_C+noaba-M058_C+noaba -0.020000000 -0.377004140 0.337004140
## M248_S+hiaba-M058_C+noaba -0.311111111 -0.677897998 0.055675776
## M248_S+lowaba-M058_C+noaba -0.342000000 -0.699004140 0.015004140
## M248_S+noaba-M058_C+noaba -0.163333333 -0.530120220 0.203453553
## M058_S+lowaba-M058_S+hiaba 0.331750000 -0.046910073 0.710410073
## M058_S+noaba-M058_S+hiaba 0.021750000 -0.356910073 0.400410073
## M248_C+hiaba-M058_S+hiaba 0.035750000 -0.342910073 0.414410073
## M248_C+lowaba-M058_S+hiaba -0.006250000 -0.419402011 0.406902011
## M248_C+noaba-M058_S+hiaba 0.193750000 -0.184910073 0.572410073
## M248_S+hiaba-M058_S+hiaba -0.097361111 -0.485258153 0.290535930
## M248_S+lowaba-M058_S+hiaba -0.128250000 -0.506910073 0.250410073
## M248_S+noaba-M058_S+hiaba 0.050416667 -0.337480375 0.438313708
## M058_S+noaba-M058_S+lowaba -0.310000000 -0.667004140 0.047004140
## M248_C+hiaba-M058_S+lowaba -0.296000000 -0.653004140 0.061004140
## M248_C+lowaba-M058_S+lowaba -0.338000000 -0.731399402 0.055399402
## M248_C+noaba-M058_S+lowaba -0.138000000 -0.495004140 0.219004140
## M248_S+hiaba-M058_S+lowaba -0.429111111 -0.795897998 -0.062324224
## M248_S+lowaba-M058_S+lowaba -0.460000000 -0.817004140 -0.102995860
## M248_S+noaba-M058_S+lowaba -0.281333333 -0.648120220 0.085453553
## M248_C+hiaba-M058_S+noaba 0.014000000 -0.343004140 0.371004140
## M248_C+lowaba-M058_S+noaba -0.028000000 -0.421399402 0.365399402
## M248_C+noaba-M058_S+noaba 0.172000000 -0.185004140 0.529004140
## M248_S+hiaba-M058_S+noaba -0.119111111 -0.485897998 0.247675776
## M248_S+lowaba-M058_S+noaba -0.150000000 -0.507004140 0.207004140
## M248_S+noaba-M058_S+noaba 0.028666667 -0.338120220 0.395453553
## M248_C+lowaba-M248_C+hiaba -0.042000000 -0.435399402 0.351399402
## M248_C+noaba-M248_C+hiaba 0.158000000 -0.199004140 0.515004140
## M248_S+hiaba-M248_C+hiaba -0.133111111 -0.499897998 0.233675776
## M248_S+lowaba-M248_C+hiaba -0.164000000 -0.521004140 0.193004140
## M248_S+noaba-M248_C+hiaba 0.014666667 -0.352120220 0.381453553
## M248_C+noaba-M248_C+lowaba 0.200000000 -0.193399402 0.593399402
## M248_S+hiaba-M248_C+lowaba -0.091111111 -0.493409202 0.311186980
## M248_S+lowaba-M248_C+lowaba -0.122000000 -0.515399402 0.271399402
## M248_S+noaba-M248_C+lowaba 0.056666667 -0.345631424 0.458964757
## M248_S+hiaba-M248_C+noaba -0.291111111 -0.657897998 0.075675776
## M248_S+lowaba-M248_C+noaba -0.322000000 -0.679004140 0.035004140
## M248_S+noaba-M248_C+noaba -0.143333333 -0.510120220 0.223453553
## M248_S+lowaba-M248_S+hiaba -0.030888889 -0.397675776 0.335897998
## M248_S+noaba-M248_S+hiaba 0.147777778 -0.228537628 0.524093183
## M248_S+noaba-M248_S+lowaba 0.178666667 -0.188120220 0.545453553
## p adj
## LA1511_C+lowaba-LA1511_C+hiaba 0.9999052
## LA1511_C+noaba-LA1511_C+hiaba 0.9999960
## LA1511_S+hiaba-LA1511_C+hiaba 0.9999889
## LA1511_S+lowaba-LA1511_C+hiaba 1.0000000
## LA1511_S+noaba-LA1511_C+hiaba 0.9998690
## M058_C+hiaba-LA1511_C+hiaba 0.3720876
## M058_C+lowaba-LA1511_C+hiaba 1.0000000
## M058_C+noaba-LA1511_C+hiaba 0.9999973
## M058_S+hiaba-LA1511_C+hiaba 0.9986116
## M058_S+lowaba-LA1511_C+hiaba 0.8780691
## M058_S+noaba-LA1511_C+hiaba 0.9996906
## M248_C+hiaba-LA1511_C+hiaba 0.9999492
## M248_C+lowaba-LA1511_C+hiaba 0.9984793
## M248_C+noaba-LA1511_C+hiaba 1.0000000
## M248_S+hiaba-LA1511_C+hiaba 0.7245568
## M248_S+lowaba-LA1511_C+hiaba 0.4552748
## M248_S+noaba-LA1511_C+hiaba 0.9999967
## LA1511_C+noaba-LA1511_C+lowaba 1.0000000
## LA1511_S+hiaba-LA1511_C+lowaba 1.0000000
## LA1511_S+lowaba-LA1511_C+lowaba 0.9999955
## LA1511_S+noaba-LA1511_C+lowaba 1.0000000
## M058_C+hiaba-LA1511_C+lowaba 0.0445258
## M058_C+lowaba-LA1511_C+lowaba 0.9938320
## M058_C+noaba-LA1511_C+lowaba 0.9477904
## M058_S+hiaba-LA1511_C+lowaba 1.0000000
## M058_S+lowaba-LA1511_C+lowaba 0.2783021
## M058_S+noaba-LA1511_C+lowaba 1.0000000
## M248_C+hiaba-LA1511_C+lowaba 1.0000000
## M248_C+lowaba-LA1511_C+lowaba 1.0000000
## M248_C+noaba-LA1511_C+lowaba 0.9815685
## M248_S+hiaba-LA1511_C+lowaba 0.9996676
## M248_S+lowaba-LA1511_C+lowaba 0.9932718
## M248_S+noaba-LA1511_C+lowaba 1.0000000
## LA1511_S+hiaba-LA1511_C+noaba 1.0000000
## LA1511_S+lowaba-LA1511_C+noaba 0.9999999
## LA1511_S+noaba-LA1511_C+noaba 1.0000000
## M058_C+hiaba-LA1511_C+noaba 0.0634537
## M058_C+lowaba-LA1511_C+noaba 0.9986715
## M058_C+noaba-LA1511_C+noaba 0.9804370
## M058_S+hiaba-LA1511_C+noaba 1.0000000
## M058_S+lowaba-LA1511_C+noaba 0.3660634
## M058_S+noaba-LA1511_C+noaba 1.0000000
## M248_C+hiaba-LA1511_C+noaba 1.0000000
## M248_C+lowaba-LA1511_C+noaba 1.0000000
## M248_C+noaba-LA1511_C+noaba 0.9950306
## M248_S+hiaba-LA1511_C+noaba 0.9955793
## M248_S+lowaba-LA1511_C+noaba 0.9596565
## M248_S+noaba-LA1511_C+noaba 1.0000000
## LA1511_S+lowaba-LA1511_S+hiaba 0.9999997
## LA1511_S+noaba-LA1511_S+hiaba 1.0000000
## M058_C+hiaba-LA1511_S+hiaba 0.1207490
## M058_C+lowaba-LA1511_S+hiaba 0.9983886
## M058_C+noaba-LA1511_S+hiaba 0.9835214
## M058_S+hiaba-LA1511_S+hiaba 1.0000000
## M058_S+lowaba-LA1511_S+hiaba 0.4732036
## M058_S+noaba-LA1511_S+hiaba 1.0000000
## M248_C+hiaba-LA1511_S+hiaba 1.0000000
## M248_C+lowaba-LA1511_S+hiaba 1.0000000
## M248_C+noaba-LA1511_S+hiaba 0.9952580
## M248_S+hiaba-LA1511_S+hiaba 0.9997607
## M248_S+lowaba-LA1511_S+hiaba 0.9956817
## M248_S+noaba-LA1511_S+hiaba 1.0000000
## LA1511_S+noaba-LA1511_S+lowaba 0.9999944
## M058_C+hiaba-LA1511_S+lowaba 0.2467050
## M058_C+lowaba-LA1511_S+lowaba 0.9999996
## M058_C+noaba-LA1511_S+lowaba 0.9999229
## M058_S+hiaba-LA1511_S+lowaba 0.9998453
## M058_S+lowaba-LA1511_S+lowaba 0.7635474
## M058_S+noaba-LA1511_S+lowaba 0.9999822
## M248_C+hiaba-LA1511_S+lowaba 0.9999985
## M248_C+lowaba-LA1511_S+lowaba 0.9998089
## M248_C+noaba-LA1511_S+lowaba 0.9999967
## M248_S+hiaba-LA1511_S+lowaba 0.8469255
## M248_S+lowaba-LA1511_S+lowaba 0.6101984
## M248_S+noaba-LA1511_S+lowaba 1.0000000
## M058_C+hiaba-LA1511_S+noaba 0.0252159
## M058_C+lowaba-LA1511_S+noaba 0.9917987
## M058_C+noaba-LA1511_S+noaba 0.9277079
## M058_S+hiaba-LA1511_S+noaba 1.0000000
## M058_S+lowaba-LA1511_S+noaba 0.2070847
## M058_S+noaba-LA1511_S+noaba 1.0000000
## M248_C+hiaba-LA1511_S+noaba 1.0000000
## M248_C+lowaba-LA1511_S+noaba 1.0000000
## M248_C+noaba-LA1511_S+noaba 0.9737227
## M248_S+hiaba-LA1511_S+noaba 0.9990035
## M248_S+lowaba-LA1511_S+noaba 0.9838643
## M248_S+noaba-LA1511_S+noaba 1.0000000
## M058_C+lowaba-M058_C+hiaba 0.8833790
## M058_C+noaba-M058_C+hiaba 0.8951317
## M058_S+hiaba-M058_C+hiaba 0.0211183
## M058_S+lowaba-M058_C+hiaba 0.9999987
## M058_S+noaba-M058_C+hiaba 0.0200513
## M248_C+hiaba-M058_C+hiaba 0.0315416
## M248_C+lowaba-M058_C+hiaba 0.0280421
## M248_C+noaba-M058_C+hiaba 0.7943358
## M248_S+hiaba-M058_C+hiaba 0.0003626
## M248_S+lowaba-M058_C+hiaba 0.0000522
## M248_S+noaba-M058_C+hiaba 0.0654597
## M058_C+noaba-M058_C+lowaba 1.0000000
## M058_S+hiaba-M058_C+lowaba 0.9737981
## M058_S+lowaba-M058_C+lowaba 0.9983626
## M058_S+noaba-M058_C+lowaba 0.9871872
## M248_C+hiaba-M058_C+lowaba 0.9949515
## M248_C+lowaba-M058_C+lowaba 0.9738113
## M248_C+noaba-M058_C+lowaba 1.0000000
## M248_S+hiaba-M058_C+lowaba 0.5004029
## M248_S+lowaba-M058_C+lowaba 0.2759829
## M248_S+noaba-M058_C+lowaba 0.9987938
## M058_S+hiaba-M058_C+noaba 0.8617111
## M058_S+lowaba-M058_C+noaba 0.9993931
## M058_S+noaba-M058_C+noaba 0.9030634
## M248_C+hiaba-M058_C+noaba 0.9476770
## M248_C+lowaba-M058_C+noaba 0.8705812
## M248_C+noaba-M058_C+noaba 1.0000000
## M248_S+hiaba-M058_C+noaba 0.2079558
## M248_S+lowaba-M058_C+noaba 0.0771617
## M248_S+noaba-M058_C+noaba 0.9817086
## M058_S+lowaba-M058_S+hiaba 0.1650045
## M058_S+noaba-M058_S+hiaba 1.0000000
## M248_C+hiaba-M058_S+hiaba 1.0000000
## M248_C+lowaba-M058_S+hiaba 1.0000000
## M248_C+noaba-M058_S+hiaba 0.9348611
## M248_S+hiaba-M058_S+hiaba 0.9999857
## M248_S+lowaba-M058_S+hiaba 0.9991740
## M248_S+noaba-M058_S+hiaba 1.0000000
## M058_S+noaba-M058_S+lowaba 0.1762561
## M248_C+hiaba-M058_S+lowaba 0.2414962
## M248_C+lowaba-M058_S+lowaba 0.1902145
## M248_C+noaba-M058_S+lowaba 0.9959739
## M248_S+hiaba-M058_S+lowaba 0.0066782
## M248_S+lowaba-M058_S+lowaba 0.0013301
## M248_S+noaba-M058_S+lowaba 0.3732182
## M248_C+hiaba-M058_S+noaba 1.0000000
## M248_C+lowaba-M058_S+noaba 1.0000000
## M248_C+noaba-M058_S+noaba 0.9613489
## M248_S+hiaba-M058_S+noaba 0.9995158
## M248_S+lowaba-M058_S+noaba 0.9899292
## M248_S+noaba-M058_S+noaba 1.0000000
## M248_C+lowaba-M248_C+hiaba 1.0000000
## M248_C+noaba-M248_C+hiaba 0.9828006
## M248_S+hiaba-M248_C+hiaba 0.9980744
## M248_S+lowaba-M248_C+hiaba 0.9752071
## M248_S+noaba-M248_C+hiaba 1.0000000
## M248_C+noaba-M248_C+lowaba 0.9382659
## M248_S+hiaba-M248_C+lowaba 0.9999968
## M248_S+lowaba-M248_C+lowaba 0.9997342
## M248_S+noaba-M248_C+lowaba 1.0000000
## M248_S+hiaba-M248_C+noaba 0.3126626
## M248_S+lowaba-M248_C+noaba 0.1314801
## M248_S+noaba-M248_C+noaba 0.9954445
## M248_S+lowaba-M248_S+hiaba 1.0000000
## M248_S+noaba-M248_S+hiaba 0.9951862
## M248_S+noaba-M248_S+lowaba 0.9573410P8 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P8)
stat.test## LA1511_C+lowaba LA1511_C+noaba LA1511_S+hiaba LA1511_S+lowaba LA1511_S+noaba
## "ab" "abc" "abc" "abc" "ab"
## M058_C+hiaba M058_C+lowaba M058_C+noaba M058_S+hiaba M058_S+lowaba
## "c" "abc" "abc" "ab" "ac"
## M058_S+noaba M248_C+hiaba M248_C+lowaba M248_C+noaba M248_S+hiaba
## "ab" "ab" "ab" "abc" "b"
## M248_S+lowaba M248_S+noaba LA1511_C+hiaba
## "b" "abc" "abc"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowaba"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
ABA_dataABA_data$All.condition <- factor(ABA_data$All.condition, levels = c("C+noaba", "C+lowaba", "C+hiaba", "S+noaba", "S+lowaba", "S+hiaba"))
#ABA_data2 <- subset(ABA_data, ABA_data$Alpha < 80)
alpha_ABA <- ggplot(data = ABA_data, mapping = aes(x = All.condition, y = Alpha, colour = All.condition))
alpha_ABA <- alpha_ABA + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
alpha_ABA <- alpha_ABA + facet_grid(~ Accession, scales = "free_y")
alpha_ABA <- alpha_ABA + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
alpha_ABA <- alpha_ABA + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
alpha_ABA <- alpha_ABA + ylab("Alpha") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 1.2)
alpha_ABA <- alpha_ABA + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
alpha_ABA <- alpha_ABA + rremove("legend")
alpha_ABA
#Now plot pareto components for the ACC treatment for 3 accessions.
list.files(pattern=".csv")## [1] "ABA-only.csv"
## [2] "ACC-only-d5excluded.csv"
## [3] "ACC-only.csv"
## [4] "cyto-only.csv"
## [5] "GA-only-d5excluded.csv"
## [6] "GA-only.csv"
## [7] "IAA-only-d5excluded.csv"
## [8] "IAA-only.csv"
## [9] "point_similarity_maryamModified.csv"
## [10] "point_similarity_maryamModified_control_Removed.csv"ACC_data <- read.csv( "ACC-only-d5excluded.csv")
ACC_dataACC_data$All.condition<-paste(ACC_data$Condition1,ACC_data$Condition2, sep="+")
ACC_dataACC_data$All.ID2<-paste(ACC_data$Accession,ACC_data$All.condition,sep="_")
ACC_dataaov(Distance.squared ~ All.ID2, data = ACC_data)## Call:
## aov(formula = Distance.squared ~ All.ID2, data = ACC_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 16065161 132276994
## Deg. of Freedom 17 139
##
## Residual standard error: 975.5168
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Distance.squared ~ All.ID2, data = ACC_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Distance.squared ~ All.ID2, data = ACC_data)
##
## $All.ID2
## diff lwr upr p adj
## LA1511_C+lowacc-LA1511_C+hiacc 1.252083e+00 -1928.4730 1930.9772 1.0000000
## LA1511_C+noacc-LA1511_C+hiacc 1.038010e+01 -1843.6398 1864.4000 1.0000000
## LA1511_S+hiacc-LA1511_C+hiacc 9.177536e-01 -1928.8073 1930.6428 1.0000000
## LA1511_S+lowacc-LA1511_C+hiacc -3.257895e-01 -1930.0509 1929.3993 1.0000000
## LA1511_S+noacc-LA1511_C+hiacc 6.348868e+00 -1847.6710 1860.3688 1.0000000
## M058_C+hiacc-LA1511_C+hiacc 4.881039e+00 -1704.4408 1714.2029 1.0000000
## M058_C+lowacc-LA1511_C+hiacc 1.365018e+03 -382.9689 3113.0045 0.3400728
## M058_C+noacc-LA1511_C+hiacc 9.539258e+00 -1699.7826 1718.8611 1.0000000
## M058_S+hiacc-LA1511_C+hiacc 1.948072e-01 -1709.1271 1709.5167 1.0000000
## M058_S+lowacc-LA1511_C+hiacc 1.120155e+00 -1708.2017 1710.4420 1.0000000
## M058_S+noacc-LA1511_C+hiacc 5.216952e+00 -1704.1049 1714.5388 1.0000000
## M248_C+hiacc-LA1511_C+hiacc 1.446128e+01 -1694.8606 1723.7832 1.0000000
## M248_C+lowacc-LA1511_C+hiacc 1.770604e+01 -1691.6158 1727.0279 1.0000000
## M248_C+noacc-LA1511_C+hiacc 3.294584e+02 -1379.8635 2038.7802 0.9999997
## M248_S+hiacc-LA1511_C+hiacc 3.175392e+00 -1706.1465 1712.4973 1.0000000
## M248_S+lowacc-LA1511_C+hiacc 9.485796e+00 -1738.5009 1757.4725 1.0000000
## M248_S+noacc-LA1511_C+hiacc 6.328565e+01 -1646.0362 1772.6075 1.0000000
## LA1511_C+noacc-LA1511_C+lowacc 9.128018e+00 -1920.5971 1938.8531 1.0000000
## LA1511_S+hiacc-LA1511_C+lowacc -3.343293e-01 -2002.9047 2002.2360 1.0000000
## LA1511_S+lowacc-LA1511_C+lowacc -1.577872e+00 -2004.1482 2000.9925 1.0000000
## LA1511_S+noacc-LA1511_C+lowacc 5.096785e+00 -1924.6283 1934.8219 1.0000000
## M058_C+hiacc-LA1511_C+lowacc 3.628956e+00 -1787.5244 1794.7823 1.0000000
## M058_C+lowacc-LA1511_C+lowacc 1.363766e+03 -464.3225 3191.8540 0.4234239
## M058_C+noacc-LA1511_C+lowacc 8.287175e+00 -1782.8662 1799.4406 1.0000000
## M058_S+hiacc-LA1511_C+lowacc -1.057276e+00 -1792.2107 1790.0961 1.0000000
## M058_S+lowacc-LA1511_C+lowacc -1.319280e-01 -1791.2853 1791.0215 1.0000000
## M058_S+noacc-LA1511_C+lowacc 3.964869e+00 -1787.1885 1795.1183 1.0000000
## M248_C+hiacc-LA1511_C+lowacc 1.320919e+01 -1777.9442 1804.3626 1.0000000
## M248_C+lowacc-LA1511_C+lowacc 1.645396e+01 -1774.6994 1807.6073 1.0000000
## M248_C+noacc-LA1511_C+lowacc 3.282063e+02 -1462.9471 2119.3597 0.9999999
## M248_S+hiacc-LA1511_C+lowacc 1.923309e+00 -1789.2301 1793.0767 1.0000000
## M248_S+lowacc-LA1511_C+lowacc 8.233713e+00 -1819.8546 1836.3220 1.0000000
## M248_S+noacc-LA1511_C+lowacc 6.203356e+01 -1729.1198 1853.1869 1.0000000
## LA1511_S+hiacc-LA1511_C+noacc -9.462347e+00 -1939.1874 1920.2627 1.0000000
## LA1511_S+lowacc-LA1511_C+noacc -1.070589e+01 -1940.4310 1919.0192 1.0000000
## LA1511_S+noacc-LA1511_C+noacc -4.031233e+00 -1858.0511 1849.9887 1.0000000
## M058_C+hiacc-LA1511_C+noacc -5.499062e+00 -1714.8209 1703.8228 1.0000000
## M058_C+lowacc-LA1511_C+noacc 1.354638e+03 -393.3490 3102.6244 0.3536461
## M058_C+noacc-LA1511_C+noacc -8.408431e-01 -1710.1627 1708.4810 1.0000000
## M058_S+hiacc-LA1511_C+noacc -1.018529e+01 -1719.5072 1699.1366 1.0000000
## M058_S+lowacc-LA1511_C+noacc -9.259946e+00 -1718.5818 1700.0619 1.0000000
## M058_S+noacc-LA1511_C+noacc -5.163149e+00 -1714.4850 1704.1587 1.0000000
## M248_C+hiacc-LA1511_C+noacc 4.081176e+00 -1705.2407 1713.4031 1.0000000
## M248_C+lowacc-LA1511_C+noacc 7.325940e+00 -1701.9959 1716.6478 1.0000000
## M248_C+noacc-LA1511_C+noacc 3.190783e+02 -1390.2436 2028.4001 0.9999998
## M248_S+hiacc-LA1511_C+noacc -7.204709e+00 -1716.5266 1702.1172 1.0000000
## M248_S+lowacc-LA1511_C+noacc -8.943054e-01 -1748.8810 1747.0924 1.0000000
## M248_S+noacc-LA1511_C+noacc 5.290555e+01 -1656.4163 1762.2274 1.0000000
## LA1511_S+lowacc-LA1511_S+hiacc -1.243543e+00 -2003.8139 2001.3268 1.0000000
## LA1511_S+noacc-LA1511_S+hiacc 5.431114e+00 -1924.2940 1935.1562 1.0000000
## M058_C+hiacc-LA1511_S+hiacc 3.963286e+00 -1787.1901 1795.1167 1.0000000
## M058_C+lowacc-LA1511_S+hiacc 1.364100e+03 -463.9882 3192.1883 0.4229668
## M058_C+noacc-LA1511_S+hiacc 8.621504e+00 -1782.5319 1799.7749 1.0000000
## M058_S+hiacc-LA1511_S+hiacc -7.229464e-01 -1791.8763 1790.4304 1.0000000
## M058_S+lowacc-LA1511_S+hiacc 2.024013e-01 -1790.9510 1791.3558 1.0000000
## M058_S+noacc-LA1511_S+hiacc 4.299199e+00 -1786.8542 1795.4526 1.0000000
## M248_C+hiacc-LA1511_S+hiacc 1.354352e+01 -1777.6099 1804.6969 1.0000000
## M248_C+lowacc-LA1511_S+hiacc 1.678829e+01 -1774.3651 1807.9417 1.0000000
## M248_C+noacc-LA1511_S+hiacc 3.285406e+02 -1462.6128 2119.6940 0.9999999
## M248_S+hiacc-LA1511_S+hiacc 2.257639e+00 -1788.8957 1793.4110 1.0000000
## M248_S+lowacc-LA1511_S+hiacc 8.568042e+00 -1819.5202 1836.6563 1.0000000
## M248_S+noacc-LA1511_S+hiacc 6.236789e+01 -1728.7855 1853.5213 1.0000000
## LA1511_S+noacc-LA1511_S+lowacc 6.674658e+00 -1923.0504 1936.3997 1.0000000
## M058_C+hiacc-LA1511_S+lowacc 5.206829e+00 -1785.9466 1796.3602 1.0000000
## M058_C+lowacc-LA1511_S+lowacc 1.365344e+03 -462.7447 3193.4319 0.4212682
## M058_C+noacc-LA1511_S+lowacc 9.865047e+00 -1781.2883 1801.0184 1.0000000
## M058_S+hiacc-LA1511_S+lowacc 5.205968e-01 -1790.6328 1791.6740 1.0000000
## M058_S+lowacc-LA1511_S+lowacc 1.445944e+00 -1789.7074 1792.5993 1.0000000
## M058_S+noacc-LA1511_S+lowacc 5.542742e+00 -1785.6106 1796.6961 1.0000000
## M248_C+hiacc-LA1511_S+lowacc 1.478707e+01 -1776.3663 1805.9405 1.0000000
## M248_C+lowacc-LA1511_S+lowacc 1.803183e+01 -1773.1216 1809.1852 1.0000000
## M248_C+noacc-LA1511_S+lowacc 3.297841e+02 -1461.3692 2120.9375 0.9999999
## M248_S+hiacc-LA1511_S+lowacc 3.501182e+00 -1787.6522 1794.6546 1.0000000
## M248_S+lowacc-LA1511_S+lowacc 9.811585e+00 -1818.2767 1837.8999 1.0000000
## M248_S+noacc-LA1511_S+lowacc 6.361144e+01 -1727.5419 1854.7648 1.0000000
## M058_C+hiacc-LA1511_S+noacc -1.467829e+00 -1710.7897 1707.8541 1.0000000
## M058_C+lowacc-LA1511_S+noacc 1.358669e+03 -389.3178 3106.6557 0.3483425
## M058_C+noacc-LA1511_S+noacc 3.190390e+00 -1706.1315 1712.5123 1.0000000
## M058_S+hiacc-LA1511_S+noacc -6.154061e+00 -1715.4759 1703.1678 1.0000000
## M058_S+lowacc-LA1511_S+noacc -5.228713e+00 -1714.5506 1704.0932 1.0000000
## M058_S+noacc-LA1511_S+noacc -1.131916e+00 -1710.4538 1708.1900 1.0000000
## M248_C+hiacc-LA1511_S+noacc 8.112409e+00 -1701.2095 1717.4343 1.0000000
## M248_C+lowacc-LA1511_S+noacc 1.135717e+01 -1697.9647 1720.6791 1.0000000
## M248_C+noacc-LA1511_S+noacc 3.231095e+02 -1386.2124 2032.4314 0.9999998
## M248_S+hiacc-LA1511_S+noacc -3.173476e+00 -1712.4954 1706.1484 1.0000000
## M248_S+lowacc-LA1511_S+noacc 3.136927e+00 -1744.8498 1751.1236 1.0000000
## M248_S+noacc-LA1511_S+noacc 5.693678e+01 -1652.3851 1766.2587 1.0000000
## M058_C+lowacc-M058_C+hiacc 1.360137e+03 -233.5536 2953.8272 0.1988637
## M058_C+noacc-M058_C+hiacc 4.658219e+00 -1546.5261 1555.8426 1.0000000
## M058_S+hiacc-M058_C+hiacc -4.686232e+00 -1555.8706 1546.4981 1.0000000
## M058_S+lowacc-M058_C+hiacc -3.760884e+00 -1554.9452 1547.4234 1.0000000
## M058_S+noacc-M058_C+hiacc 3.359131e-01 -1550.8484 1551.5202 1.0000000
## M248_C+hiacc-M058_C+hiacc 9.580238e+00 -1541.6041 1560.7646 1.0000000
## M248_C+lowacc-M058_C+hiacc 1.282500e+01 -1538.3593 1564.0093 1.0000000
## M248_C+noacc-M058_C+hiacc 3.245773e+02 -1226.6070 1875.7617 0.9999990
## M248_S+hiacc-M058_C+hiacc -1.705647e+00 -1552.8900 1549.4787 1.0000000
## M248_S+lowacc-M058_C+hiacc 4.604756e+00 -1589.0856 1598.2952 1.0000000
## M248_S+noacc-M058_C+hiacc 5.840461e+01 -1492.7797 1609.5889 1.0000000
## M058_C+noacc-M058_C+lowacc -1.355479e+03 -2949.1690 238.2118 0.2036208
## M058_S+hiacc-M058_C+lowacc -1.364823e+03 -2958.5134 228.8674 0.1941580
## M058_S+lowacc-M058_C+lowacc -1.363898e+03 -2957.5881 229.7927 0.1950809
## M058_S+noacc-M058_C+lowacc -1.359801e+03 -2953.4913 233.8895 0.1992041
## M248_C+hiacc-M058_C+lowacc -1.350557e+03 -2944.2470 243.1339 0.2087337
## M248_C+lowacc-M058_C+lowacc -1.347312e+03 -2941.0022 246.3786 0.2121529
## M248_C+noacc-M058_C+lowacc -1.035559e+03 -2629.2499 558.1309 0.6744169
## M248_S+hiacc-M058_C+lowacc -1.361842e+03 -2955.5328 231.8480 0.1971417
## M248_S+lowacc-M058_C+lowacc -1.355532e+03 -2990.6239 279.5598 0.2410657
## M248_S+noacc-M058_C+lowacc -1.301732e+03 -2895.4226 291.9582 0.2642614
## M058_S+hiacc-M058_C+noacc -9.344451e+00 -1560.5288 1541.8399 1.0000000
## M058_S+lowacc-M058_C+noacc -8.419103e+00 -1559.6034 1542.7652 1.0000000
## M058_S+noacc-M058_C+noacc -4.322305e+00 -1555.5066 1546.8620 1.0000000
## M248_C+hiacc-M058_C+noacc 4.922019e+00 -1546.2623 1556.1064 1.0000000
## M248_C+lowacc-M058_C+noacc 8.166783e+00 -1543.0176 1559.3511 1.0000000
## M248_C+noacc-M058_C+noacc 3.199191e+02 -1231.2652 1871.1034 0.9999992
## M248_S+hiacc-M058_C+noacc -6.363866e+00 -1557.5482 1544.8205 1.0000000
## M248_S+lowacc-M058_C+noacc -5.346236e-02 -1593.7439 1593.6369 1.0000000
## M248_S+noacc-M058_C+noacc 5.374639e+01 -1497.4379 1604.9307 1.0000000
## M058_S+lowacc-M058_S+hiacc 9.253477e-01 -1550.2590 1552.1097 1.0000000
## M058_S+noacc-M058_S+hiacc 5.022145e+00 -1546.1622 1556.2065 1.0000000
## M248_C+hiacc-M058_S+hiacc 1.426647e+01 -1536.9179 1565.4508 1.0000000
## M248_C+lowacc-M058_S+hiacc 1.751123e+01 -1533.6731 1568.6956 1.0000000
## M248_C+noacc-M058_S+hiacc 3.292635e+02 -1221.9208 1880.4479 0.9999988
## M248_S+hiacc-M058_S+hiacc 2.980585e+00 -1548.2037 1554.1649 1.0000000
## M248_S+lowacc-M058_S+hiacc 9.290988e+00 -1584.3994 1602.9814 1.0000000
## M248_S+noacc-M058_S+hiacc 6.309084e+01 -1488.0935 1614.2752 1.0000000
## M058_S+noacc-M058_S+lowacc 4.096797e+00 -1547.0875 1555.2811 1.0000000
## M248_C+hiacc-M058_S+lowacc 1.334112e+01 -1537.8432 1564.5255 1.0000000
## M248_C+lowacc-M058_S+lowacc 1.658589e+01 -1534.5984 1567.7702 1.0000000
## M248_C+noacc-M058_S+lowacc 3.283382e+02 -1222.8461 1879.5225 0.9999988
## M248_S+hiacc-M058_S+lowacc 2.055237e+00 -1549.1291 1553.2396 1.0000000
## M248_S+lowacc-M058_S+lowacc 8.365641e+00 -1585.3248 1602.0560 1.0000000
## M248_S+noacc-M058_S+lowacc 6.216549e+01 -1489.0188 1613.3498 1.0000000
## M248_C+hiacc-M058_S+noacc 9.244325e+00 -1541.9400 1560.4287 1.0000000
## M248_C+lowacc-M058_S+noacc 1.248909e+01 -1538.6952 1563.6734 1.0000000
## M248_C+noacc-M058_S+noacc 3.242414e+02 -1226.9429 1875.4257 0.9999990
## M248_S+hiacc-M058_S+noacc -2.041560e+00 -1553.2259 1549.1428 1.0000000
## M248_S+lowacc-M058_S+noacc 4.268843e+00 -1589.4216 1597.9592 1.0000000
## M248_S+noacc-M058_S+noacc 5.806869e+01 -1493.1156 1609.2530 1.0000000
## M248_C+lowacc-M248_C+hiacc 3.244764e+00 -1547.9396 1554.4291 1.0000000
## M248_C+noacc-M248_C+hiacc 3.149971e+02 -1236.1873 1866.1814 0.9999994
## M248_S+hiacc-M248_C+hiacc -1.128589e+01 -1562.4702 1539.8984 1.0000000
## M248_S+lowacc-M248_C+hiacc -4.975482e+00 -1598.6659 1588.7149 1.0000000
## M248_S+noacc-M248_C+hiacc 4.882437e+01 -1502.3600 1600.0087 1.0000000
## M248_C+noacc-M248_C+lowacc 3.117523e+02 -1239.4320 1862.9366 0.9999995
## M248_S+hiacc-M248_C+lowacc -1.453065e+01 -1565.7150 1536.6537 1.0000000
## M248_S+lowacc-M248_C+lowacc -8.220246e+00 -1601.9107 1585.4702 1.0000000
## M248_S+noacc-M248_C+lowacc 4.557961e+01 -1505.6047 1596.7639 1.0000000
## M248_S+hiacc-M248_C+noacc -3.262830e+02 -1877.4673 1224.9014 0.9999989
## M248_S+lowacc-M248_C+noacc -3.199726e+02 -1913.6630 1273.7178 0.9999995
## M248_S+noacc-M248_C+noacc -2.661727e+02 -1817.3570 1285.0116 1.0000000
## M248_S+lowacc-M248_S+hiacc 6.310403e+00 -1587.3800 1600.0008 1.0000000
## M248_S+noacc-M248_S+hiacc 6.011025e+01 -1491.0741 1611.2946 1.0000000
## M248_S+noacc-M248_S+lowacc 5.379985e+01 -1539.8906 1647.4903 1.0000000P7 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P7)
stat.test## $Letters
## LA1511_C+lowacc LA1511_C+noacc LA1511_S+hiacc LA1511_S+lowacc LA1511_S+noacc
## "a" "a" "a" "a" "a"
## M058_C+hiacc M058_C+lowacc M058_C+noacc M058_S+hiacc M058_S+lowacc
## "a" "a" "a" "a" "a"
## M058_S+noacc M248_C+hiacc M248_C+lowacc M248_C+noacc M248_S+hiacc
## "a" "a" "a" "a" "a"
## M248_S+lowacc M248_S+noacc LA1511_C+hiacc
## "a" "a" "a"
##
## $LetterMatrix
## a
## LA1511_C+lowacc TRUE
## LA1511_C+noacc TRUE
## LA1511_S+hiacc TRUE
## LA1511_S+lowacc TRUE
## LA1511_S+noacc TRUE
## M058_C+hiacc TRUE
## M058_C+lowacc TRUE
## M058_C+noacc TRUE
## M058_S+hiacc TRUE
## M058_S+lowacc TRUE
## M058_S+noacc TRUE
## M248_C+hiacc TRUE
## M248_C+lowacc TRUE
## M248_C+noacc TRUE
## M248_S+hiacc TRUE
## M248_S+lowacc TRUE
## M248_S+noacc TRUE
## LA1511_C+hiacc TRUEtest <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowacc"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
ACC_dataACC_data$All.condition <- factor(ACC_data$All.condition, levels = c("C+noacc", "C+lowacc", "C+hiacc", "S+noacc", "S+lowacc", "S+hiacc"))
ACC_data2 <- subset(ACC_data, ACC_data$Distance.squared < 750)
distance_ACC <- ggplot(data = ACC_data2, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_ACC <- distance_ACC + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_ACC <- distance_ACC + facet_grid(~ Accession, scales = "free_y")
distance_ACC <- distance_ACC + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_ACC <- distance_ACC + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
distance_ACC <- distance_ACC + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey",y.position = 750)
distance_ACC <- distance_ACC + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_ACC <- distance_ACC + rremove("legend")
distance_ACC
#I wanted to regraph this time < 100 because there are so much variation in the C+noacc
ACC_data$All.condition <- factor(ACC_data$All.condition, levels = c("C+noacc", "C+lowacc", "C+hiacc", "S+noacc", "S+lowacc", "S+hiacc"))
ACC_data2 <- subset(ACC_data, ACC_data$Distance.squared < 25)
distance_ACC <- ggplot(data = ACC_data2, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_ACC <- distance_ACC + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_ACC <- distance_ACC + facet_grid(~ Accession, scales = "free_y")
distance_ACC <- distance_ACC + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_ACC <- distance_ACC + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
distance_ACC <- distance_ACC + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey",y.position = 25)
distance_ACC <- distance_ACC + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_ACC <- distance_ACC + rremove("legend")
distance_ACC
aov(Alpha ~ All.ID2, data = ACC_data)## Call:
## aov(formula = Alpha ~ All.ID2, data = ACC_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 2.23025 5.90223
## Deg. of Freedom 17 139
##
## Residual standard error: 0.2060633
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Alpha ~ All.ID2, data = ACC_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Alpha ~ All.ID2, data = ACC_data)
##
## $All.ID2
## diff lwr upr
## LA1511_C+lowacc-LA1511_C+hiacc -8.095238e-03 -0.41572074 0.399530267
## LA1511_C+noacc-LA1511_C+hiacc -2.371429e-01 -0.62877677 0.154491060
## LA1511_S+hiacc-LA1511_C+hiacc -2.309524e-02 -0.43072074 0.384530267
## LA1511_S+lowacc-LA1511_C+hiacc 6.023810e-02 -0.34738741 0.467863600
## LA1511_S+noacc-LA1511_C+hiacc -2.242857e-01 -0.61591963 0.167348203
## M058_C+hiacc-LA1511_C+hiacc -5.428571e-03 -0.36649720 0.355640060
## M058_C+lowacc-LA1511_C+hiacc -2.142857e-02 -0.39066457 0.347807427
## M058_C+noacc-LA1511_C+hiacc 9.057143e-02 -0.27049720 0.451640060
## M058_S+hiacc-LA1511_C+hiacc -4.842857e-02 -0.40949720 0.312640060
## M058_S+lowacc-LA1511_C+hiacc 2.857143e-02 -0.33249720 0.389640060
## M058_S+noacc-LA1511_C+hiacc -2.474286e-01 -0.60849720 0.113640060
## M248_C+hiacc-LA1511_C+hiacc -7.242857e-02 -0.43349720 0.288640060
## M248_C+lowacc-LA1511_C+hiacc 1.657143e-02 -0.34449720 0.377640060
## M248_C+noacc-LA1511_C+hiacc -2.684286e-01 -0.62949720 0.092640060
## M248_S+hiacc-LA1511_C+hiacc 4.157143e-02 -0.31949720 0.402640060
## M248_S+lowacc-LA1511_C+hiacc 2.857143e-02 -0.34066457 0.397807427
## M248_S+noacc-LA1511_C+hiacc -2.384286e-01 -0.59949720 0.122640060
## LA1511_C+noacc-LA1511_C+lowacc -2.290476e-01 -0.63667312 0.178577886
## LA1511_S+hiacc-LA1511_C+lowacc -1.500000e-02 -0.43801298 0.408012978
## LA1511_S+lowacc-LA1511_C+lowacc 6.833333e-02 -0.35467964 0.491346311
## LA1511_S+noacc-LA1511_C+lowacc -2.161905e-01 -0.62381598 0.191435029
## M058_C+hiacc-LA1511_C+lowacc 2.666667e-03 -0.37568764 0.381020976
## M058_C+lowacc-LA1511_C+lowacc -1.333333e-02 -0.39948958 0.372822917
## M058_C+noacc-LA1511_C+lowacc 9.866667e-02 -0.27968764 0.477020976
## M058_S+hiacc-LA1511_C+lowacc -4.033333e-02 -0.41868764 0.338020976
## M058_S+lowacc-LA1511_C+lowacc 3.666667e-02 -0.34168764 0.415020976
## M058_S+noacc-LA1511_C+lowacc -2.393333e-01 -0.61768764 0.139020976
## M248_C+hiacc-LA1511_C+lowacc -6.433333e-02 -0.44268764 0.314020976
## M248_C+lowacc-LA1511_C+lowacc 2.466667e-02 -0.35368764 0.403020976
## M248_C+noacc-LA1511_C+lowacc -2.603333e-01 -0.63868764 0.118020976
## M248_S+hiacc-LA1511_C+lowacc 4.966667e-02 -0.32868764 0.428020976
## M248_S+lowacc-LA1511_C+lowacc 3.666667e-02 -0.34948958 0.422822917
## M248_S+noacc-LA1511_C+lowacc -2.303333e-01 -0.60868764 0.148020976
## LA1511_S+hiacc-LA1511_C+noacc 2.140476e-01 -0.19357789 0.621673124
## LA1511_S+lowacc-LA1511_C+noacc 2.973810e-01 -0.11024455 0.705006457
## LA1511_S+noacc-LA1511_C+noacc 1.285714e-02 -0.37877677 0.404491060
## M058_C+hiacc-LA1511_C+noacc 2.317143e-01 -0.12935435 0.592782917
## M058_C+lowacc-LA1511_C+noacc 2.157143e-01 -0.15352171 0.584950284
## M058_C+noacc-LA1511_C+noacc 3.277143e-01 -0.03335435 0.688782917
## M058_S+hiacc-LA1511_C+noacc 1.887143e-01 -0.17235435 0.549782917
## M058_S+lowacc-LA1511_C+noacc 2.657143e-01 -0.09535435 0.626782917
## M058_S+noacc-LA1511_C+noacc -1.028571e-02 -0.37135435 0.350782917
## M248_C+hiacc-LA1511_C+noacc 1.647143e-01 -0.19635435 0.525782917
## M248_C+lowacc-LA1511_C+noacc 2.537143e-01 -0.10735435 0.614782917
## M248_C+noacc-LA1511_C+noacc -3.128571e-02 -0.39235435 0.329782917
## M248_S+hiacc-LA1511_C+noacc 2.787143e-01 -0.08235435 0.639782917
## M248_S+lowacc-LA1511_C+noacc 2.657143e-01 -0.10352171 0.634950284
## M248_S+noacc-LA1511_C+noacc -1.285714e-03 -0.36235435 0.359782917
## LA1511_S+lowacc-LA1511_S+hiacc 8.333333e-02 -0.33967964 0.506346311
## LA1511_S+noacc-LA1511_S+hiacc -2.011905e-01 -0.60881598 0.206435029
## M058_C+hiacc-LA1511_S+hiacc 1.766667e-02 -0.36068764 0.396020976
## M058_C+lowacc-LA1511_S+hiacc 1.666667e-03 -0.38448958 0.387822917
## M058_C+noacc-LA1511_S+hiacc 1.136667e-01 -0.26468764 0.492020976
## M058_S+hiacc-LA1511_S+hiacc -2.533333e-02 -0.40368764 0.353020976
## M058_S+lowacc-LA1511_S+hiacc 5.166667e-02 -0.32668764 0.430020976
## M058_S+noacc-LA1511_S+hiacc -2.243333e-01 -0.60268764 0.154020976
## M248_C+hiacc-LA1511_S+hiacc -4.933333e-02 -0.42768764 0.329020976
## M248_C+lowacc-LA1511_S+hiacc 3.966667e-02 -0.33868764 0.418020976
## M248_C+noacc-LA1511_S+hiacc -2.453333e-01 -0.62368764 0.133020976
## M248_S+hiacc-LA1511_S+hiacc 6.466667e-02 -0.31368764 0.443020976
## M248_S+lowacc-LA1511_S+hiacc 5.166667e-02 -0.33448958 0.437822917
## M248_S+noacc-LA1511_S+hiacc -2.153333e-01 -0.59368764 0.163020976
## LA1511_S+noacc-LA1511_S+lowacc -2.845238e-01 -0.69214931 0.123101696
## M058_C+hiacc-LA1511_S+lowacc -6.566667e-02 -0.44402098 0.312687643
## M058_C+lowacc-LA1511_S+lowacc -8.166667e-02 -0.46782292 0.304489584
## M058_C+noacc-LA1511_S+lowacc 3.033333e-02 -0.34802098 0.408687643
## M058_S+hiacc-LA1511_S+lowacc -1.086667e-01 -0.48702098 0.269687643
## M058_S+lowacc-LA1511_S+lowacc -3.166667e-02 -0.41002098 0.346687643
## M058_S+noacc-LA1511_S+lowacc -3.076667e-01 -0.68602098 0.070687643
## M248_C+hiacc-LA1511_S+lowacc -1.326667e-01 -0.51102098 0.245687643
## M248_C+lowacc-LA1511_S+lowacc -4.366667e-02 -0.42202098 0.334687643
## M248_C+noacc-LA1511_S+lowacc -3.286667e-01 -0.70702098 0.049687643
## M248_S+hiacc-LA1511_S+lowacc -1.866667e-02 -0.39702098 0.359687643
## M248_S+lowacc-LA1511_S+lowacc -3.166667e-02 -0.41782292 0.354489584
## M248_S+noacc-LA1511_S+lowacc -2.986667e-01 -0.67702098 0.079687643
## M058_C+hiacc-LA1511_S+noacc 2.188571e-01 -0.14221149 0.579925774
## M058_C+lowacc-LA1511_S+noacc 2.028571e-01 -0.16637886 0.572093141
## M058_C+noacc-LA1511_S+noacc 3.148571e-01 -0.04621149 0.675925774
## M058_S+hiacc-LA1511_S+noacc 1.758571e-01 -0.18521149 0.536925774
## M058_S+lowacc-LA1511_S+noacc 2.528571e-01 -0.10821149 0.613925774
## M058_S+noacc-LA1511_S+noacc -2.314286e-02 -0.38421149 0.337925774
## M248_C+hiacc-LA1511_S+noacc 1.518571e-01 -0.20921149 0.512925774
## M248_C+lowacc-LA1511_S+noacc 2.408571e-01 -0.12021149 0.601925774
## M248_C+noacc-LA1511_S+noacc -4.414286e-02 -0.40521149 0.316925774
## M248_S+hiacc-LA1511_S+noacc 2.658571e-01 -0.09521149 0.626925774
## M248_S+lowacc-LA1511_S+noacc 2.528571e-01 -0.11637886 0.622093141
## M248_S+noacc-LA1511_S+noacc -1.414286e-02 -0.37521149 0.346925774
## M058_C+lowacc-M058_C+hiacc -1.600000e-02 -0.35264321 0.320643214
## M058_C+noacc-M058_C+hiacc 9.600000e-02 -0.23166444 0.423664444
## M058_S+hiacc-M058_C+hiacc -4.300000e-02 -0.37066444 0.284664444
## M058_S+lowacc-M058_C+hiacc 3.400000e-02 -0.29366444 0.361664444
## M058_S+noacc-M058_C+hiacc -2.420000e-01 -0.56966444 0.085664444
## M248_C+hiacc-M058_C+hiacc -6.700000e-02 -0.39466444 0.260664444
## M248_C+lowacc-M058_C+hiacc 2.200000e-02 -0.30566444 0.349664444
## M248_C+noacc-M058_C+hiacc -2.630000e-01 -0.59066444 0.064664444
## M248_S+hiacc-M058_C+hiacc 4.700000e-02 -0.28066444 0.374664444
## M248_S+lowacc-M058_C+hiacc 3.400000e-02 -0.30264321 0.370643214
## M248_S+noacc-M058_C+hiacc -2.330000e-01 -0.56066444 0.094664444
## M058_C+noacc-M058_C+lowacc 1.120000e-01 -0.22464321 0.448643214
## M058_S+hiacc-M058_C+lowacc -2.700000e-02 -0.36364321 0.309643214
## M058_S+lowacc-M058_C+lowacc 5.000000e-02 -0.28664321 0.386643214
## M058_S+noacc-M058_C+lowacc -2.260000e-01 -0.56264321 0.110643214
## M248_C+hiacc-M058_C+lowacc -5.100000e-02 -0.38764321 0.285643214
## M248_C+lowacc-M058_C+lowacc 3.800000e-02 -0.29864321 0.374643214
## M248_C+noacc-M058_C+lowacc -2.470000e-01 -0.58364321 0.089643214
## M248_S+hiacc-M058_C+lowacc 6.300000e-02 -0.27364321 0.399643214
## M248_S+lowacc-M058_C+lowacc 5.000000e-02 -0.29538865 0.395388650
## M248_S+noacc-M058_C+lowacc -2.170000e-01 -0.55364321 0.119643214
## M058_S+hiacc-M058_C+noacc -1.390000e-01 -0.46666444 0.188664444
## M058_S+lowacc-M058_C+noacc -6.200000e-02 -0.38966444 0.265664444
## M058_S+noacc-M058_C+noacc -3.380000e-01 -0.66566444 -0.010335556
## M248_C+hiacc-M058_C+noacc -1.630000e-01 -0.49066444 0.164664444
## M248_C+lowacc-M058_C+noacc -7.400000e-02 -0.40166444 0.253664444
## M248_C+noacc-M058_C+noacc -3.590000e-01 -0.68666444 -0.031335556
## M248_S+hiacc-M058_C+noacc -4.900000e-02 -0.37666444 0.278664444
## M248_S+lowacc-M058_C+noacc -6.200000e-02 -0.39864321 0.274643214
## M248_S+noacc-M058_C+noacc -3.290000e-01 -0.65666444 -0.001335556
## M058_S+lowacc-M058_S+hiacc 7.700000e-02 -0.25066444 0.404664444
## M058_S+noacc-M058_S+hiacc -1.990000e-01 -0.52666444 0.128664444
## M248_C+hiacc-M058_S+hiacc -2.400000e-02 -0.35166444 0.303664444
## M248_C+lowacc-M058_S+hiacc 6.500000e-02 -0.26266444 0.392664444
## M248_C+noacc-M058_S+hiacc -2.200000e-01 -0.54766444 0.107664444
## M248_S+hiacc-M058_S+hiacc 9.000000e-02 -0.23766444 0.417664444
## M248_S+lowacc-M058_S+hiacc 7.700000e-02 -0.25964321 0.413643214
## M248_S+noacc-M058_S+hiacc -1.900000e-01 -0.51766444 0.137664444
## M058_S+noacc-M058_S+lowacc -2.760000e-01 -0.60366444 0.051664444
## M248_C+hiacc-M058_S+lowacc -1.010000e-01 -0.42866444 0.226664444
## M248_C+lowacc-M058_S+lowacc -1.200000e-02 -0.33966444 0.315664444
## M248_C+noacc-M058_S+lowacc -2.970000e-01 -0.62466444 0.030664444
## M248_S+hiacc-M058_S+lowacc 1.300000e-02 -0.31466444 0.340664444
## M248_S+lowacc-M058_S+lowacc 1.110223e-16 -0.33664321 0.336643214
## M248_S+noacc-M058_S+lowacc -2.670000e-01 -0.59466444 0.060664444
## M248_C+hiacc-M058_S+noacc 1.750000e-01 -0.15266444 0.502664444
## M248_C+lowacc-M058_S+noacc 2.640000e-01 -0.06366444 0.591664444
## M248_C+noacc-M058_S+noacc -2.100000e-02 -0.34866444 0.306664444
## M248_S+hiacc-M058_S+noacc 2.890000e-01 -0.03866444 0.616664444
## M248_S+lowacc-M058_S+noacc 2.760000e-01 -0.06064321 0.612643214
## M248_S+noacc-M058_S+noacc 9.000000e-03 -0.31866444 0.336664444
## M248_C+lowacc-M248_C+hiacc 8.900000e-02 -0.23866444 0.416664444
## M248_C+noacc-M248_C+hiacc -1.960000e-01 -0.52366444 0.131664444
## M248_S+hiacc-M248_C+hiacc 1.140000e-01 -0.21366444 0.441664444
## M248_S+lowacc-M248_C+hiacc 1.010000e-01 -0.23564321 0.437643214
## M248_S+noacc-M248_C+hiacc -1.660000e-01 -0.49366444 0.161664444
## M248_C+noacc-M248_C+lowacc -2.850000e-01 -0.61266444 0.042664444
## M248_S+hiacc-M248_C+lowacc 2.500000e-02 -0.30266444 0.352664444
## M248_S+lowacc-M248_C+lowacc 1.200000e-02 -0.32464321 0.348643214
## M248_S+noacc-M248_C+lowacc -2.550000e-01 -0.58266444 0.072664444
## M248_S+hiacc-M248_C+noacc 3.100000e-01 -0.01766444 0.637664444
## M248_S+lowacc-M248_C+noacc 2.970000e-01 -0.03964321 0.633643214
## M248_S+noacc-M248_C+noacc 3.000000e-02 -0.29766444 0.357664444
## M248_S+lowacc-M248_S+hiacc -1.300000e-02 -0.34964321 0.323643214
## M248_S+noacc-M248_S+hiacc -2.800000e-01 -0.60766444 0.047664444
## M248_S+noacc-M248_S+lowacc -2.670000e-01 -0.60364321 0.069643214
## p adj
## LA1511_C+lowacc-LA1511_C+hiacc 1.0000000
## LA1511_C+noacc-LA1511_C+hiacc 0.7799718
## LA1511_S+hiacc-LA1511_C+hiacc 1.0000000
## LA1511_S+lowacc-LA1511_C+hiacc 1.0000000
## LA1511_S+noacc-LA1511_C+hiacc 0.8461603
## M058_C+hiacc-LA1511_C+hiacc 1.0000000
## M058_C+lowacc-LA1511_C+hiacc 1.0000000
## M058_C+noacc-LA1511_C+hiacc 0.9999855
## M058_S+hiacc-LA1511_C+hiacc 1.0000000
## M058_S+lowacc-LA1511_C+hiacc 1.0000000
## M058_S+noacc-LA1511_C+hiacc 0.5818637
## M248_C+hiacc-LA1511_C+hiacc 0.9999995
## M248_C+lowacc-LA1511_C+hiacc 1.0000000
## M248_C+noacc-LA1511_C+hiacc 0.4298879
## M248_S+hiacc-LA1511_C+hiacc 1.0000000
## M248_S+lowacc-LA1511_C+hiacc 1.0000000
## M248_S+noacc-LA1511_C+hiacc 0.6473372
## LA1511_C+noacc-LA1511_C+lowacc 0.8651412
## LA1511_S+hiacc-LA1511_C+lowacc 1.0000000
## LA1511_S+lowacc-LA1511_C+lowacc 1.0000000
## LA1511_S+noacc-LA1511_C+lowacc 0.9122398
## M058_C+hiacc-LA1511_C+lowacc 1.0000000
## M058_C+lowacc-LA1511_C+lowacc 1.0000000
## M058_C+noacc-LA1511_C+lowacc 0.9999748
## M058_S+hiacc-LA1511_C+lowacc 1.0000000
## M058_S+lowacc-LA1511_C+lowacc 1.0000000
## M058_S+noacc-LA1511_C+lowacc 0.7172709
## M248_C+hiacc-LA1511_C+lowacc 1.0000000
## M248_C+lowacc-LA1511_C+lowacc 1.0000000
## M248_C+noacc-LA1511_C+lowacc 0.5744366
## M248_S+hiacc-LA1511_C+lowacc 1.0000000
## M248_S+lowacc-LA1511_C+lowacc 1.0000000
## M248_S+noacc-LA1511_C+lowacc 0.7727763
## LA1511_S+hiacc-LA1511_C+noacc 0.9188650
## LA1511_S+lowacc-LA1511_C+noacc 0.4652616
## LA1511_S+noacc-LA1511_C+noacc 1.0000000
## M058_C+hiacc-LA1511_C+noacc 0.6946584
## M058_C+lowacc-LA1511_C+noacc 0.8243165
## M058_C+noacc-LA1511_C+noacc 0.1246588
## M058_S+hiacc-LA1511_C+noacc 0.9218393
## M058_S+lowacc-LA1511_C+noacc 0.4489296
## M058_S+noacc-LA1511_C+noacc 1.0000000
## M248_C+hiacc-LA1511_C+noacc 0.9765367
## M248_C+lowacc-LA1511_C+noacc 0.5356729
## M248_C+noacc-LA1511_C+noacc 1.0000000
## M248_S+hiacc-LA1511_C+noacc 0.3607343
## M248_S+lowacc-LA1511_C+noacc 0.4910047
## M248_S+noacc-LA1511_C+noacc 1.0000000
## LA1511_S+lowacc-LA1511_S+hiacc 0.9999996
## LA1511_S+noacc-LA1511_S+hiacc 0.9515915
## M058_C+hiacc-LA1511_S+hiacc 1.0000000
## M058_C+lowacc-LA1511_S+hiacc 1.0000000
## M058_C+noacc-LA1511_S+hiacc 0.9998220
## M058_S+hiacc-LA1511_S+hiacc 1.0000000
## M058_S+lowacc-LA1511_S+hiacc 1.0000000
## M058_S+noacc-LA1511_S+hiacc 0.8068039
## M248_C+hiacc-LA1511_S+hiacc 1.0000000
## M248_C+lowacc-LA1511_S+hiacc 1.0000000
## M248_C+noacc-LA1511_S+hiacc 0.6778786
## M248_S+hiacc-LA1511_S+hiacc 1.0000000
## M248_S+lowacc-LA1511_S+hiacc 1.0000000
## M248_S+noacc-LA1511_S+hiacc 0.8525856
## LA1511_S+noacc-LA1511_S+lowacc 0.5480641
## M058_C+hiacc-LA1511_S+lowacc 0.9999999
## M058_C+lowacc-LA1511_S+lowacc 0.9999988
## M058_C+noacc-LA1511_S+lowacc 1.0000000
## M058_S+hiacc-LA1511_S+lowacc 0.9999031
## M058_S+lowacc-LA1511_S+lowacc 1.0000000
## M058_S+noacc-LA1511_S+lowacc 0.2714203
## M248_C+hiacc-LA1511_S+lowacc 0.9987076
## M248_C+lowacc-LA1511_S+lowacc 1.0000000
## M248_C+noacc-LA1511_S+lowacc 0.1753643
## M248_S+hiacc-LA1511_S+lowacc 1.0000000
## M248_S+lowacc-LA1511_S+lowacc 1.0000000
## M248_S+noacc-LA1511_S+lowacc 0.3211852
## M058_C+hiacc-LA1511_S+noacc 0.7786193
## M058_C+lowacc-LA1511_S+noacc 0.8853333
## M058_C+noacc-LA1511_S+noacc 0.1704918
## M058_S+hiacc-LA1511_S+noacc 0.9569407
## M058_S+lowacc-LA1511_S+noacc 0.5419652
## M058_S+noacc-LA1511_S+noacc 1.0000000
## M248_C+hiacc-LA1511_S+noacc 0.9896802
## M248_C+lowacc-LA1511_S+noacc 0.6298364
## M248_C+noacc-LA1511_S+noacc 1.0000000
## M248_S+hiacc-LA1511_S+noacc 0.4479205
## M248_S+lowacc-LA1511_S+noacc 0.5830718
## M248_S+noacc-LA1511_S+noacc 1.0000000
## M058_C+lowacc-M058_C+hiacc 1.0000000
## M058_C+noacc-M058_C+hiacc 0.9998730
## M058_S+hiacc-M058_C+hiacc 1.0000000
## M058_S+lowacc-M058_C+hiacc 1.0000000
## M058_S+noacc-M058_C+hiacc 0.4421859
## M248_C+hiacc-M058_C+hiacc 0.9999993
## M248_C+lowacc-M058_C+hiacc 1.0000000
## M248_C+noacc-M058_C+hiacc 0.2928207
## M248_S+hiacc-M058_C+hiacc 1.0000000
## M248_S+lowacc-M058_C+hiacc 1.0000000
## M248_S+noacc-M058_C+hiacc 0.5134243
## M058_C+noacc-M058_C+lowacc 0.9993279
## M058_S+hiacc-M058_C+lowacc 1.0000000
## M058_S+lowacc-M058_C+lowacc 1.0000000
## M058_S+noacc-M058_C+lowacc 0.6186581
## M248_C+hiacc-M058_C+lowacc 1.0000000
## M248_C+lowacc-M058_C+lowacc 1.0000000
## M248_C+noacc-M058_C+lowacc 0.4545439
## M248_S+hiacc-M058_C+lowacc 0.9999998
## M248_S+lowacc-M058_C+lowacc 1.0000000
## M248_S+noacc-M058_C+lowacc 0.6875188
## M058_S+hiacc-M058_C+noacc 0.9887037
## M058_S+lowacc-M058_C+noacc 0.9999998
## M058_S+noacc-M058_C+noacc 0.0354929
## M248_C+hiacc-M058_C+noacc 0.9481770
## M248_C+lowacc-M058_C+noacc 0.9999969
## M248_C+noacc-M058_C+noacc 0.0169365
## M248_S+hiacc-M058_C+noacc 1.0000000
## M248_S+lowacc-M058_C+noacc 0.9999999
## M248_S+noacc-M058_C+noacc 0.0478742
## M058_S+lowacc-M058_S+hiacc 0.9999944
## M058_S+noacc-M058_S+hiacc 0.7759906
## M248_C+hiacc-M058_S+hiacc 1.0000000
## M248_C+lowacc-M058_S+hiacc 0.9999996
## M248_C+noacc-M058_S+hiacc 0.6184356
## M248_S+hiacc-M058_S+hiacc 0.9999476
## M248_S+lowacc-M058_S+hiacc 0.9999962
## M248_S+noacc-M058_S+hiacc 0.8327582
## M058_S+noacc-M058_S+lowacc 0.2173964
## M248_C+hiacc-M058_S+lowacc 0.9997496
## M248_C+lowacc-M058_S+lowacc 1.0000000
## M248_C+noacc-M058_S+lowacc 0.1260373
## M248_S+hiacc-M058_S+lowacc 1.0000000
## M248_S+lowacc-M058_S+lowacc 1.0000000
## M248_S+noacc-M058_S+lowacc 0.2680806
## M248_C+hiacc-M058_S+noacc 0.9073451
## M248_C+lowacc-M058_S+noacc 0.2865112
## M248_C+noacc-M058_S+noacc 1.0000000
## M248_S+hiacc-M058_S+noacc 0.1565253
## M248_S+lowacc-M058_S+noacc 0.2583335
## M248_S+noacc-M058_S+noacc 1.0000000
## M248_C+lowacc-M248_C+hiacc 0.9999552
## M248_C+noacc-M248_C+hiacc 0.7958216
## M248_S+hiacc-M248_C+hiacc 0.9988255
## M248_S+lowacc-M248_C+hiacc 0.9998252
## M248_S+noacc-M248_C+hiacc 0.9394724
## M248_C+noacc-M248_C+lowacc 0.1737222
## M248_S+hiacc-M248_C+lowacc 1.0000000
## M248_S+lowacc-M248_C+lowacc 1.0000000
## M248_S+noacc-M248_C+lowacc 0.3461497
## M248_S+hiacc-M248_C+noacc 0.0866811
## M248_S+lowacc-M248_C+noacc 0.1562009
## M248_S+noacc-M248_C+noacc 1.0000000
## M248_S+lowacc-M248_S+hiacc 1.0000000
## M248_S+noacc-M248_S+hiacc 0.1971234
## M248_S+noacc-M248_S+lowacc 0.3130354P8 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P8)
stat.test## LA1511_C+lowacc LA1511_C+noacc LA1511_S+hiacc LA1511_S+lowacc LA1511_S+noacc
## "ab" "ab" "ab" "ab" "ab"
## M058_C+hiacc M058_C+lowacc M058_C+noacc M058_S+hiacc M058_S+lowacc
## "ab" "ab" "a" "ab" "ab"
## M058_S+noacc M248_C+hiacc M248_C+lowacc M248_C+noacc M248_S+hiacc
## "b" "ab" "ab" "b" "ab"
## M248_S+lowacc M248_S+noacc LA1511_C+hiacc
## "ab" "b" "ab"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowacc"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
ACC_dataACC_data$All.condition <- factor(ACC_data$All.condition, levels = c("C+noacc", "C+lowacc", "C+hiacc", "S+noacc", "S+lowacc", "S+hiacc"))
ACC_data2 <- subset(ACC_data, ACC_data$Alpha < 10)
Alpha_ACC <- ggplot(data = ACC_data2, mapping = aes(x = All.condition, y = Alpha, colour = All.condition))
Alpha_ACC <- Alpha_ACC + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Alpha_ACC <- Alpha_ACC + facet_grid(~ Accession, scales = "free_y")
Alpha_ACC <- Alpha_ACC + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Alpha_ACC <- Alpha_ACC + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
Alpha_ACC <- Alpha_ACC + ylab("Alpha") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 1.2)
Alpha_ACC <- Alpha_ACC + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Alpha_ACC <- Alpha_ACC + rremove("legend")
Alpha_ACC
#plot IAA
list.files(pattern=".csv")## [1] "ABA-only.csv"
## [2] "ACC-only-d5excluded.csv"
## [3] "ACC-only.csv"
## [4] "cyto-only.csv"
## [5] "GA-only-d5excluded.csv"
## [6] "GA-only.csv"
## [7] "IAA-only-d5excluded.csv"
## [8] "IAA-only.csv"
## [9] "point_similarity_maryamModified.csv"
## [10] "point_similarity_maryamModified_control_Removed.csv"IAA_data <- read.csv("IAA-only-d5excluded.csv")
IAA_dataIAA_data$All.condition<-paste(IAA_data$Condition1,IAA_data$Condition2, sep="+")
IAA_dataIAA_data$All.ID2<-paste(IAA_data$Accession,IAA_data$All.condition,sep="_")
IAA_dataaov(Distance.squared ~ All.ID2, data = IAA_data)## Call:
## aov(formula = Distance.squared ~ All.ID2, data = IAA_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 1527.906 9515.560
## Deg. of Freedom 11 100
##
## Residual standard error: 9.754773
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Distance.squared ~ All.ID2, data = IAA_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Distance.squared ~ All.ID2, data = IAA_data)
##
## $All.ID2
## diff lwr upr p adj
## LA1511_C+noiaa-LA1511_C+iaa -1.7222123 -19.603916 16.159491 1.0000000
## LA1511_S+iaa-LA1511_C+iaa -9.5818199 -24.582253 5.418613 0.5974402
## LA1511_S+noiaa-LA1511_C+iaa -9.4113295 -24.897339 6.074680 0.6694453
## M058_C+iaa-LA1511_C+iaa -4.4973600 -19.097710 10.102990 0.9965887
## M058_C+noiaa-LA1511_C+iaa -11.4106497 -26.010999 3.189700 0.2853944
## M058_S+iaa-LA1511_C+iaa -9.3629300 -23.963280 5.237420 0.5915263
## M058_S+noiaa-LA1511_C+iaa -13.5092533 -28.109603 1.091096 0.0976618
## M248_C+iaa-LA1511_C+iaa -7.9778793 -22.578229 6.622470 0.7982709
## M248_C+noiaa-LA1511_C+iaa -9.7757477 -24.376097 4.824602 0.5248239
## M248_S+iaa-LA1511_C+iaa -7.7624372 -22.362787 6.837913 0.8251125
## M248_S+noiaa-LA1511_C+iaa -10.5227735 -25.123123 4.077576 0.4079271
## LA1511_S+iaa-LA1511_C+noiaa -7.8596076 -26.069443 10.350228 0.9513789
## LA1511_S+noiaa-LA1511_C+noiaa -7.6891172 -26.300984 10.922750 0.9642733
## M058_C+iaa-LA1511_C+noiaa -2.7751477 -20.656851 15.106556 0.9999956
## M058_C+noiaa-LA1511_C+noiaa -9.6884374 -27.570141 8.193266 0.8068613
## M058_S+iaa-LA1511_C+noiaa -7.6407177 -25.522421 10.240986 0.9546536
## M058_S+noiaa-LA1511_C+noiaa -11.7870410 -29.668744 6.094662 0.5493042
## M248_C+iaa-LA1511_C+noiaa -6.2556670 -24.137370 11.626036 0.9900274
## M248_C+noiaa-LA1511_C+noiaa -8.0535354 -25.935239 9.828168 0.9351950
## M248_S+iaa-LA1511_C+noiaa -6.0402249 -23.921928 11.841479 0.9925222
## M248_S+noiaa-LA1511_C+noiaa -8.8005612 -26.682265 9.081142 0.8868729
## LA1511_S+noiaa-LA1511_S+iaa 0.1704904 -15.693282 16.034263 1.0000000
## M058_C+iaa-LA1511_S+iaa 5.0844599 -9.915973 20.084893 0.9923054
## M058_C+noiaa-LA1511_S+iaa -1.8288298 -16.829263 13.171604 0.9999997
## M058_S+iaa-LA1511_S+iaa 0.2188899 -14.781543 15.219323 1.0000000
## M058_S+noiaa-LA1511_S+iaa -3.9274334 -18.927867 11.073000 0.9992125
## M248_C+iaa-LA1511_S+iaa 1.6039406 -13.396493 16.604374 0.9999999
## M248_C+noiaa-LA1511_S+iaa -0.1939278 -15.194361 14.806506 1.0000000
## M248_S+iaa-LA1511_S+iaa 1.8193827 -13.181051 16.819816 0.9999997
## M248_S+noiaa-LA1511_S+iaa -0.9409536 -15.941387 14.059480 1.0000000
## M058_C+iaa-LA1511_S+noiaa 4.9139695 -10.572040 20.399979 0.9955896
## M058_C+noiaa-LA1511_S+noiaa -1.9993202 -17.485330 13.486689 0.9999994
## M058_S+iaa-LA1511_S+noiaa 0.0483995 -15.437610 15.534409 1.0000000
## M058_S+noiaa-LA1511_S+noiaa -4.0979238 -19.583933 11.388086 0.9991308
## M248_C+iaa-LA1511_S+noiaa 1.4334502 -14.052559 16.919460 1.0000000
## M248_C+noiaa-LA1511_S+noiaa -0.3644182 -15.850428 15.121591 1.0000000
## M248_S+iaa-LA1511_S+noiaa 1.6488923 -13.837117 17.134902 0.9999999
## M248_S+noiaa-LA1511_S+noiaa -1.1114440 -16.597453 14.374565 1.0000000
## M058_C+noiaa-M058_C+iaa -6.9132897 -21.513639 7.687060 0.9106098
## M058_S+iaa-M058_C+iaa -4.8655700 -19.465920 9.734780 0.9933192
## M058_S+noiaa-M058_C+iaa -9.0118933 -23.612243 5.588456 0.6476737
## M248_C+iaa-M058_C+iaa -3.4805193 -18.080869 11.119830 0.9996751
## M248_C+noiaa-M058_C+iaa -5.2783877 -19.878737 9.321962 0.9870097
## M248_S+iaa-M058_C+iaa -3.2650772 -17.865427 11.335273 0.9998247
## M248_S+noiaa-M058_C+iaa -6.0254135 -20.625763 8.574936 0.9645459
## M058_S+iaa-M058_C+noiaa 2.0477197 -12.552630 16.648069 0.9999985
## M058_S+noiaa-M058_C+noiaa -2.0986036 -16.698953 12.501746 0.9999980
## M248_C+iaa-M058_C+noiaa 3.4327704 -11.167579 18.033120 0.9997155
## M248_C+noiaa-M058_C+noiaa 1.6349020 -12.965448 16.235252 0.9999999
## M248_S+iaa-M058_C+noiaa 3.6482125 -10.952137 18.248562 0.9994918
## M248_S+noiaa-M058_C+noiaa 0.8878762 -13.712474 15.488226 1.0000000
## M058_S+noiaa-M058_S+iaa -4.1463233 -18.746673 10.454026 0.9983412
## M248_C+iaa-M058_S+iaa 1.3850507 -13.215299 15.985400 1.0000000
## M248_C+noiaa-M058_S+iaa -0.4128177 -15.013167 14.187532 1.0000000
## M248_S+iaa-M058_S+iaa 1.6004928 -12.999857 16.200843 0.9999999
## M248_S+noiaa-M058_S+iaa -1.1598435 -15.760193 13.440506 1.0000000
## M248_C+iaa-M058_S+noiaa 5.5313740 -9.068976 20.131724 0.9812564
## M248_C+noiaa-M058_S+noiaa 3.7335056 -10.866844 18.333855 0.9993683
## M248_S+iaa-M058_S+noiaa 5.7468161 -8.853534 20.347166 0.9749482
## M248_S+noiaa-M058_S+noiaa 2.9864798 -11.613870 17.586830 0.9999271
## M248_C+noiaa-M248_C+iaa -1.7978684 -16.398218 12.802481 0.9999996
## M248_S+iaa-M248_C+iaa 0.2154421 -14.384908 14.815792 1.0000000
## M248_S+noiaa-M248_C+iaa -2.5448942 -17.145244 12.055456 0.9999855
## M248_S+iaa-M248_C+noiaa 2.0133105 -12.587039 16.613660 0.9999987
## M248_S+noiaa-M248_C+noiaa -0.7470258 -15.347376 13.853324 1.0000000
## M248_S+noiaa-M248_S+iaa -2.7603363 -17.360686 11.840013 0.9999669P7 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P7)
stat.test## $Letters
## LA1511_C+noiaa LA1511_S+iaa LA1511_S+noiaa M058_C+iaa M058_C+noiaa
## "a" "a" "a" "a" "a"
## M058_S+iaa M058_S+noiaa M248_C+iaa M248_C+noiaa M248_S+iaa
## "a" "a" "a" "a" "a"
## M248_S+noiaa LA1511_C+iaa
## "a" "a"
##
## $LetterMatrix
## a
## LA1511_C+noiaa TRUE
## LA1511_S+iaa TRUE
## LA1511_S+noiaa TRUE
## M058_C+iaa TRUE
## M058_C+noiaa TRUE
## M058_S+iaa TRUE
## M058_S+noiaa TRUE
## M248_C+iaa TRUE
## M248_C+noiaa TRUE
## M248_S+iaa TRUE
## M248_S+noiaa TRUE
## LA1511_C+iaa TRUEtest <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+noiaa"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
IAA_dataIAA_data$All.condition <- factor(IAA_data$All.condition, levels = c("C+noiaa", "C+iaa", "S+noiaa", "S+iaa"))
IAA_data2 <- subset(IAA_data, IAA_data$Distance.squared < 15)
distance_IAA <- ggplot(data = IAA_data2, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_IAA <- distance_IAA + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_IAA <- distance_IAA + facet_grid(~ Accession, scales = "free_y")
distance_IAA <- distance_IAA + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_IAA <- distance_IAA + scale_color_manual(values = c("blueviolet","cyan", "red1","green"))
distance_IAA <- distance_IAA + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 15)
distance_IAA <- distance_IAA + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_IAA <- distance_IAA + rremove("legend")
distance_IAA
aov(Alpha ~ All.ID2, data = IAA_data)## Call:
## aov(formula = Alpha ~ All.ID2, data = IAA_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 1.012331 4.466096
## Deg. of Freedom 11 100
##
## Residual standard error: 0.2113314
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Alpha ~ All.ID2, data = IAA_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Alpha ~ All.ID2, data = IAA_data)
##
## $All.ID2
## diff lwr upr p adj
## LA1511_C+noiaa-LA1511_C+iaa 0.057000000 -0.3303966 0.444396551 0.9999975
## LA1511_S+iaa-LA1511_C+iaa -0.003888889 -0.3288644 0.321086647 1.0000000
## LA1511_S+noiaa-LA1511_C+iaa 0.076250000 -0.2592453 0.411745254 0.9997949
## M058_C+iaa-LA1511_C+iaa 0.113000000 -0.2033080 0.429307959 0.9881882
## M058_C+noiaa-LA1511_C+iaa 0.066000000 -0.2503080 0.382307959 0.9999112
## M058_S+iaa-LA1511_C+iaa -0.133000000 -0.4493080 0.183307959 0.9594919
## M058_S+noiaa-LA1511_C+iaa -0.024000000 -0.3403080 0.292307959 1.0000000
## M248_C+iaa-LA1511_C+iaa -0.131000000 -0.4473080 0.185307959 0.9636334
## M248_C+noiaa-LA1511_C+iaa -0.201000000 -0.5173080 0.115307959 0.6052286
## M248_S+iaa-LA1511_C+iaa -0.070000000 -0.3863080 0.246307959 0.9998417
## M248_S+noiaa-LA1511_C+iaa -0.107000000 -0.4233080 0.209307959 0.9924318
## LA1511_S+iaa-LA1511_C+noiaa -0.060888889 -0.4553942 0.333616449 0.9999959
## LA1511_S+noiaa-LA1511_C+noiaa 0.019250000 -0.3839651 0.422465114 1.0000000
## M058_C+iaa-LA1511_C+noiaa 0.056000000 -0.3313966 0.443396551 0.9999979
## M058_C+noiaa-LA1511_C+noiaa 0.009000000 -0.3783966 0.396396551 1.0000000
## M058_S+iaa-LA1511_C+noiaa -0.190000000 -0.5773966 0.197396551 0.8891837
## M058_S+noiaa-LA1511_C+noiaa -0.081000000 -0.4683966 0.306396551 0.9999094
## M248_C+iaa-LA1511_C+noiaa -0.188000000 -0.5753966 0.199396551 0.8960175
## M248_C+noiaa-LA1511_C+noiaa -0.258000000 -0.6453966 0.129396551 0.5332286
## M248_S+iaa-LA1511_C+noiaa -0.127000000 -0.5143966 0.260396551 0.9941792
## M248_S+noiaa-LA1511_C+noiaa -0.164000000 -0.5513966 0.223396551 0.9575081
## LA1511_S+noiaa-LA1511_S+iaa 0.080138889 -0.2635404 0.423818157 0.9997372
## M058_C+iaa-LA1511_S+iaa 0.116888889 -0.2080866 0.441864424 0.9875273
## M058_C+noiaa-LA1511_S+iaa 0.069888889 -0.2550866 0.394864424 0.9998804
## M058_S+iaa-LA1511_S+iaa -0.129111111 -0.4540866 0.195864424 0.9731458
## M058_S+noiaa-LA1511_S+iaa -0.020111111 -0.3450866 0.304864424 1.0000000
## M248_C+iaa-LA1511_S+iaa -0.127111111 -0.4520866 0.197864424 0.9761022
## M248_C+noiaa-LA1511_S+iaa -0.197111111 -0.5220866 0.127864424 0.6721462
## M248_S+iaa-LA1511_S+iaa -0.066111111 -0.3910866 0.258864424 0.9999310
## M248_S+noiaa-LA1511_S+iaa -0.103111111 -0.4280866 0.221864424 0.9955929
## M058_C+iaa-LA1511_S+noiaa 0.036750000 -0.2987453 0.372245254 0.9999999
## M058_C+noiaa-LA1511_S+noiaa -0.010250000 -0.3457453 0.325245254 1.0000000
## M058_S+iaa-LA1511_S+noiaa -0.209250000 -0.5447453 0.126245254 0.6326992
## M058_S+noiaa-LA1511_S+noiaa -0.100250000 -0.4357453 0.235245254 0.9973869
## M248_C+iaa-LA1511_S+noiaa -0.207250000 -0.5427453 0.128245254 0.6465080
## M248_C+noiaa-LA1511_S+noiaa -0.277250000 -0.6127453 0.058245254 0.2110574
## M248_S+iaa-LA1511_S+noiaa -0.146250000 -0.4817453 0.189245254 0.9479481
## M248_S+noiaa-LA1511_S+noiaa -0.183250000 -0.5187453 0.152245254 0.7986654
## M058_C+noiaa-M058_C+iaa -0.047000000 -0.3633080 0.269307959 0.9999972
## M058_S+iaa-M058_C+iaa -0.246000000 -0.5623080 0.070307959 0.2923738
## M058_S+noiaa-M058_C+iaa -0.137000000 -0.4533080 0.179307959 0.9501966
## M248_C+iaa-M058_C+iaa -0.244000000 -0.5603080 0.072307959 0.3041794
## M248_C+noiaa-M058_C+iaa -0.314000000 -0.6303080 0.002307959 0.0535403
## M248_S+iaa-M058_C+iaa -0.183000000 -0.4993080 0.133307959 0.7337357
## M248_S+noiaa-M058_C+iaa -0.220000000 -0.5363080 0.096307959 0.4644424
## M058_S+iaa-M058_C+noiaa -0.199000000 -0.5153080 0.117307959 0.6200441
## M058_S+noiaa-M058_C+noiaa -0.090000000 -0.4063080 0.226307959 0.9983123
## M248_C+iaa-M058_C+noiaa -0.197000000 -0.5133080 0.119307959 0.6347764
## M248_C+noiaa-M058_C+noiaa -0.267000000 -0.5833080 0.049307959 0.1857460
## M248_S+iaa-M058_C+noiaa -0.136000000 -0.4523080 0.180307959 0.9526507
## M248_S+noiaa-M058_C+noiaa -0.173000000 -0.4893080 0.143307959 0.7972936
## M058_S+noiaa-M058_S+iaa 0.109000000 -0.2073080 0.425307959 0.9911827
## M248_C+iaa-M058_S+iaa 0.002000000 -0.3143080 0.318307959 1.0000000
## M248_C+noiaa-M058_S+iaa -0.068000000 -0.3843080 0.248307959 0.9998808
## M248_S+iaa-M058_S+iaa 0.063000000 -0.2533080 0.379307959 0.9999441
## M248_S+noiaa-M058_S+iaa 0.026000000 -0.2903080 0.342307959 1.0000000
## M248_C+iaa-M058_S+noiaa -0.107000000 -0.4233080 0.209307959 0.9924318
## M248_C+noiaa-M058_S+noiaa -0.177000000 -0.4933080 0.139307959 0.7727703
## M248_S+iaa-M058_S+noiaa -0.046000000 -0.3623080 0.270307959 0.9999978
## M248_S+noiaa-M058_S+noiaa -0.083000000 -0.3993080 0.233307959 0.9991961
## M248_C+noiaa-M248_C+iaa -0.070000000 -0.3863080 0.246307959 0.9998417
## M248_S+iaa-M248_C+iaa 0.061000000 -0.2553080 0.377307959 0.9999595
## M248_S+noiaa-M248_C+iaa 0.024000000 -0.2923080 0.340307959 1.0000000
## M248_S+iaa-M248_C+noiaa 0.131000000 -0.1853080 0.447307959 0.9636334
## M248_S+noiaa-M248_C+noiaa 0.094000000 -0.2223080 0.410307959 0.9975106
## M248_S+noiaa-M248_S+iaa -0.037000000 -0.3533080 0.279307959 0.9999998P8 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P8)
stat.test## $Letters
## LA1511_C+noiaa LA1511_S+iaa LA1511_S+noiaa M058_C+iaa M058_C+noiaa
## "a" "a" "a" "a" "a"
## M058_S+iaa M058_S+noiaa M248_C+iaa M248_C+noiaa M248_S+iaa
## "a" "a" "a" "a" "a"
## M248_S+noiaa LA1511_C+iaa
## "a" "a"
##
## $LetterMatrix
## a
## LA1511_C+noiaa TRUE
## LA1511_S+iaa TRUE
## LA1511_S+noiaa TRUE
## M058_C+iaa TRUE
## M058_C+noiaa TRUE
## M058_S+iaa TRUE
## M058_S+noiaa TRUE
## M248_C+iaa TRUE
## M248_C+noiaa TRUE
## M248_S+iaa TRUE
## M248_S+noiaa TRUE
## LA1511_C+iaa TRUEtest <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+noiaa"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
IAA_dataIAA_data$All.condition <- factor(IAA_data$All.condition, levels = c("C+noiaa", "C+iaa", "S+noiaa", "S+iaa"))
Alpha_IAA <- ggplot(data = IAA_data, mapping = aes(x = All.condition, y = Alpha, colour = All.condition))
Alpha_IAA <- Alpha_IAA + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Alpha_IAA <- Alpha_IAA + facet_grid(~ Accession, scales = "free_y")
Alpha_IAA <- Alpha_IAA + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Alpha_IAA <- Alpha_IAA + scale_color_manual(values = c("blueviolet","cyan", "red1","green"))
Alpha_IAA <- Alpha_IAA + ylab("Alpha") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 1)
Alpha_IAA <- Alpha_IAA + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Alpha_IAA <- Alpha_IAA + rremove("legend")
Alpha_IAA
list.files(pattern = ".csv")## [1] "ABA-only.csv"
## [2] "ACC-only-d5excluded.csv"
## [3] "ACC-only.csv"
## [4] "cyto-only.csv"
## [5] "GA-only-d5excluded.csv"
## [6] "GA-only.csv"
## [7] "IAA-only-d5excluded.csv"
## [8] "IAA-only.csv"
## [9] "point_similarity_maryamModified.csv"
## [10] "point_similarity_maryamModified_control_Removed.csv"GA_data <- read.csv("GA-only-d5excluded.csv")
GA_dataGA_data$All.condition<-paste(GA_data$Condition1,GA_data$Condition2, sep="+")
GA_dataGA_data$All.ID2<-paste(GA_data$Accession,GA_data$All.condition,sep="_")
GA_dataaov(Distance.squared ~ All.ID2, data = GA_data)## Call:
## aov(formula = Distance.squared ~ All.ID2, data = GA_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 917437.2 1794703.5
## Deg. of Freedom 17 163
##
## Residual standard error: 104.9307
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Distance.squared ~ All.ID2, data = GA_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Distance.squared ~ All.ID2, data = GA_data)
##
## $All.ID2
## diff lwr upr p adj
## LA1511_C+lowga-LA1511_C+higa -20.1437738 -182.706093 142.41855 1.0000000
## LA1511_C+noga-LA1511_C+higa -22.5593832 -185.121702 140.00294 1.0000000
## LA1511_S+higa-LA1511_C+higa -20.3235383 -178.968117 138.32104 1.0000000
## LA1511_S+lowga-LA1511_C+higa -35.7256202 -194.370199 122.91896 0.9999973
## LA1511_S+noga-LA1511_C+higa -34.0235306 -201.249600 133.20254 0.9999994
## M058_C+higa-LA1511_C+higa -20.6372620 -183.199581 141.92506 1.0000000
## M058_C+lowga-LA1511_C+higa -24.9890932 -187.551412 137.57323 1.0000000
## M058_C+noga-LA1511_C+higa -31.1807661 -193.743085 131.38155 0.9999998
## M058_S+higa-LA1511_C+higa -34.5082646 -197.070584 128.05405 0.9999989
## M058_S+lowga-LA1511_C+higa -31.2903047 -193.852624 131.27201 0.9999997
## M058_S+noga-LA1511_C+higa -36.5007177 -203.726787 130.72535 0.9999983
## M248_C+higa-LA1511_C+higa -8.9291187 -171.491438 153.63320 1.0000000
## M248_C+lowga-LA1511_C+higa 73.4216094 -89.140710 235.98393 0.9796270
## M248_C+noga-LA1511_C+higa -11.3464575 -173.908776 151.21586 1.0000000
## M248_S+higa-LA1511_C+higa 98.4516331 -64.110686 261.01395 0.7840924
## M248_S+lowga-LA1511_C+higa 259.7490931 97.186774 422.31141 0.0000096
## M248_S+noga-LA1511_C+higa -13.9233627 -176.485682 148.63896 1.0000000
## LA1511_C+noga-LA1511_C+lowga -2.4156094 -168.803447 163.97223 1.0000000
## LA1511_S+higa-LA1511_C+lowga -0.1797645 -162.742083 162.38255 1.0000000
## LA1511_S+lowga-LA1511_C+lowga -15.5818464 -178.144165 146.98047 1.0000000
## LA1511_S+noga-LA1511_C+lowga -13.8797568 -184.827010 157.06750 1.0000000
## M058_C+higa-LA1511_C+lowga -0.4934882 -166.881326 165.89435 1.0000000
## M058_C+lowga-LA1511_C+lowga -4.8453194 -171.233157 161.54252 1.0000000
## M058_C+noga-LA1511_C+lowga -11.0369923 -177.424830 155.35085 1.0000000
## M058_S+higa-LA1511_C+lowga -14.3644908 -180.752329 152.02335 1.0000000
## M058_S+lowga-LA1511_C+lowga -11.1465309 -177.534369 155.24131 1.0000000
## M058_S+noga-LA1511_C+lowga -16.3569439 -187.304197 154.59031 1.0000000
## M248_C+higa-LA1511_C+lowga 11.2146551 -155.173183 177.60249 1.0000000
## M248_C+lowga-LA1511_C+lowga 93.5653832 -72.822455 259.95322 0.8678649
## M248_C+noga-LA1511_C+lowga 8.7973163 -157.590522 175.18515 1.0000000
## M248_S+higa-LA1511_C+lowga 118.5954069 -47.792431 284.98324 0.5135175
## M248_S+lowga-LA1511_C+lowga 279.8928669 113.505029 446.28070 0.0000022
## M248_S+noga-LA1511_C+lowga 6.2204111 -160.167427 172.60825 1.0000000
## LA1511_S+higa-LA1511_C+noga 2.2358449 -160.326474 164.79816 1.0000000
## LA1511_S+lowga-LA1511_C+noga -13.1662370 -175.728556 149.39608 1.0000000
## LA1511_S+noga-LA1511_C+noga -11.4641474 -182.411400 159.48311 1.0000000
## M058_C+higa-LA1511_C+noga 1.9221212 -164.465717 168.30996 1.0000000
## M058_C+lowga-LA1511_C+noga -2.4297100 -168.817548 163.95813 1.0000000
## M058_C+noga-LA1511_C+noga -8.6213829 -175.009221 157.76646 1.0000000
## M058_S+higa-LA1511_C+noga -11.9488814 -178.336719 154.43896 1.0000000
## M058_S+lowga-LA1511_C+noga -8.7309215 -175.118760 157.65692 1.0000000
## M058_S+noga-LA1511_C+noga -13.9413345 -184.888588 157.00592 1.0000000
## M248_C+higa-LA1511_C+noga 13.6302645 -152.757574 180.01810 1.0000000
## M248_C+lowga-LA1511_C+noga 95.9809926 -70.406845 262.36883 0.8422443
## M248_C+noga-LA1511_C+noga 11.2129257 -155.174912 177.60076 1.0000000
## M248_S+higa-LA1511_C+noga 121.0110163 -45.376822 287.39885 0.4753889
## M248_S+lowga-LA1511_C+noga 282.3084763 115.920638 448.69631 0.0000017
## M248_S+noga-LA1511_C+noga 8.6360205 -157.751818 175.02386 1.0000000
## LA1511_S+lowga-LA1511_S+higa -15.4020819 -174.046661 143.24250 1.0000000
## LA1511_S+noga-LA1511_S+higa -13.6999923 -180.926062 153.52608 1.0000000
## M058_C+higa-LA1511_S+higa -0.3137237 -162.876043 162.24860 1.0000000
## M058_C+lowga-LA1511_S+higa -4.6655549 -167.227874 157.89676 1.0000000
## M058_C+noga-LA1511_S+higa -10.8572278 -173.419547 151.70509 1.0000000
## M058_S+higa-LA1511_S+higa -14.1847263 -176.747045 148.37759 1.0000000
## M058_S+lowga-LA1511_S+higa -10.9667664 -173.529085 151.59555 1.0000000
## M058_S+noga-LA1511_S+higa -16.1771794 -183.403249 151.04889 1.0000000
## M248_C+higa-LA1511_S+higa 11.3944196 -151.167899 173.95674 1.0000000
## M248_C+lowga-LA1511_S+higa 93.7451477 -68.817171 256.30747 0.8425759
## M248_C+noga-LA1511_S+higa 8.9770808 -153.585238 171.53940 1.0000000
## M248_S+higa-LA1511_S+higa 118.7751714 -43.787148 281.33749 0.4666586
## M248_S+lowga-LA1511_S+higa 280.0726314 117.510312 442.63495 0.0000011
## M248_S+noga-LA1511_S+higa 6.4001756 -156.162143 168.96249 1.0000000
## LA1511_S+noga-LA1511_S+lowga 1.7020896 -165.523980 168.92816 1.0000000
## M058_C+higa-LA1511_S+lowga 15.0883582 -147.473961 177.65068 1.0000000
## M058_C+lowga-LA1511_S+lowga 10.7365270 -151.825792 173.29885 1.0000000
## M058_C+noga-LA1511_S+lowga 4.5448541 -158.017465 167.10717 1.0000000
## M058_S+higa-LA1511_S+lowga 1.2173556 -161.344963 163.77967 1.0000000
## M058_S+lowga-LA1511_S+lowga 4.4353155 -158.127003 166.99763 1.0000000
## M058_S+noga-LA1511_S+lowga -0.7750975 -168.001167 166.45097 1.0000000
## M248_C+higa-LA1511_S+lowga 26.7965015 -135.765817 189.35882 1.0000000
## M248_C+lowga-LA1511_S+lowga 109.1472296 -53.415089 271.70955 0.6232628
## M248_C+noga-LA1511_S+lowga 24.3791627 -138.183156 186.94148 1.0000000
## M248_S+higa-LA1511_S+lowga 134.1772533 -28.385066 296.73957 0.2500824
## M248_S+lowga-LA1511_S+lowga 295.4747133 132.912394 458.03703 0.0000002
## M248_S+noga-LA1511_S+lowga 21.8022575 -140.760061 184.36458 1.0000000
## M058_C+higa-LA1511_S+noga 13.3862686 -157.560985 184.33352 1.0000000
## M058_C+lowga-LA1511_S+noga 9.0344374 -161.912816 179.98169 1.0000000
## M058_C+noga-LA1511_S+noga 2.8427645 -168.104489 173.79002 1.0000000
## M058_S+higa-LA1511_S+noga -0.4847340 -171.431987 170.46252 1.0000000
## M058_S+lowga-LA1511_S+noga 2.7332259 -168.214027 173.68048 1.0000000
## M058_S+noga-LA1511_S+noga -2.4771871 -177.865368 172.91099 1.0000000
## M248_C+higa-LA1511_S+noga 25.0944119 -145.852841 196.04166 1.0000000
## M248_C+lowga-LA1511_S+noga 107.4451400 -63.502113 278.39239 0.7316732
## M248_C+noga-LA1511_S+noga 22.6770731 -148.270180 193.62433 1.0000000
## M248_S+higa-LA1511_S+noga 132.4751637 -38.472089 303.42242 0.3570638
## M248_S+lowga-LA1511_S+noga 293.7726237 122.825371 464.71988 0.0000012
## M248_S+noga-LA1511_S+noga 20.1001679 -150.847085 191.04742 1.0000000
## M058_C+lowga-M058_C+higa -4.3518312 -170.739669 162.03601 1.0000000
## M058_C+noga-M058_C+higa -10.5435041 -176.931342 155.84433 1.0000000
## M058_S+higa-M058_C+higa -13.8710026 -180.258841 152.51684 1.0000000
## M058_S+lowga-M058_C+higa -10.6530427 -177.040881 155.73480 1.0000000
## M058_S+noga-M058_C+higa -15.8634557 -186.810709 155.08380 1.0000000
## M248_C+higa-M058_C+higa 11.7081433 -154.679695 178.09598 1.0000000
## M248_C+lowga-M058_C+higa 94.0588714 -72.328967 260.44671 0.8628441
## M248_C+noga-M058_C+higa 9.2908045 -157.097034 175.67864 1.0000000
## M248_S+higa-M058_C+higa 119.0888951 -47.298943 285.47673 0.5056819
## M248_S+lowga-M058_C+higa 280.3863551 113.998517 446.77419 0.0000021
## M248_S+noga-M058_C+higa 6.7138993 -159.673939 173.10174 1.0000000
## M058_C+noga-M058_C+lowga -6.1916729 -172.579511 160.19617 1.0000000
## M058_S+higa-M058_C+lowga -9.5191714 -175.907009 156.86867 1.0000000
## M058_S+lowga-M058_C+lowga -6.3012115 -172.689050 160.08663 1.0000000
## M058_S+noga-M058_C+lowga -11.5116245 -182.458878 159.43563 1.0000000
## M248_C+higa-M058_C+lowga 16.0599745 -150.327864 182.44781 1.0000000
## M248_C+lowga-M058_C+lowga 98.4107026 -67.977135 264.79854 0.8139013
## M248_C+noga-M058_C+lowga 13.6426357 -152.745202 180.03047 1.0000000
## M248_S+higa-M058_C+lowga 123.4407263 -42.947112 289.82856 0.4378054
## M248_S+lowga-M058_C+lowga 284.7381863 118.350348 451.12602 0.0000013
## M248_S+noga-M058_C+lowga 11.0657305 -155.322108 177.45357 1.0000000
## M058_S+higa-M058_C+noga -3.3274985 -169.715337 163.06034 1.0000000
## M058_S+lowga-M058_C+noga -0.1095386 -166.497377 166.27830 1.0000000
## M058_S+noga-M058_C+noga -5.3199516 -176.267205 165.62730 1.0000000
## M248_C+higa-M058_C+noga 22.2516474 -144.136191 188.63949 1.0000000
## M248_C+lowga-M058_C+noga 104.6023755 -61.785463 270.99021 0.7313434
## M248_C+noga-M058_C+noga 19.8343086 -146.553529 186.22215 1.0000000
## M248_S+higa-M058_C+noga 129.6323992 -36.755439 296.02024 0.3474582
## M248_S+lowga-M058_C+noga 290.9298592 124.542021 457.31770 0.0000007
## M248_S+noga-M058_C+noga 17.2574034 -149.130435 183.64524 1.0000000
## M058_S+lowga-M058_S+higa 3.2179599 -163.169878 169.60580 1.0000000
## M058_S+noga-M058_S+higa -1.9924531 -172.939706 168.95480 1.0000000
## M248_C+higa-M058_S+higa 25.5791459 -140.808692 191.96698 1.0000000
## M248_C+lowga-M058_S+higa 107.9298740 -58.457964 274.31771 0.6820669
## M248_C+noga-M058_S+higa 23.1618071 -143.226031 189.54965 1.0000000
## M248_S+higa-M058_S+higa 132.9598977 -33.427940 299.34774 0.3031064
## M248_S+lowga-M058_S+higa 294.2573577 127.869520 460.64520 0.0000005
## M248_S+noga-M058_S+higa 20.5849019 -145.802936 186.97274 1.0000000
## M058_S+noga-M058_S+lowga -5.2104130 -176.157666 165.73684 1.0000000
## M248_C+higa-M058_S+lowga 22.3611860 -144.026652 188.74902 1.0000000
## M248_C+lowga-M058_S+lowga 104.7119141 -61.675924 271.09975 0.7297676
## M248_C+noga-M058_S+lowga 19.9438472 -146.443991 186.33169 1.0000000
## M248_S+higa-M058_S+lowga 129.7419378 -36.645900 296.12978 0.3459467
## M248_S+lowga-M058_S+lowga 291.0393978 124.651560 457.42724 0.0000007
## M248_S+noga-M058_S+lowga 17.3669420 -149.020896 183.75478 1.0000000
## M248_C+higa-M058_S+noga 27.5715990 -143.375654 198.51885 1.0000000
## M248_C+lowga-M058_S+noga 109.9223271 -61.024926 280.86958 0.6962514
## M248_C+noga-M058_S+noga 25.1542602 -145.792993 196.10151 1.0000000
## M248_S+higa-M058_S+noga 134.9523508 -35.994902 305.89960 0.3241131
## M248_S+lowga-M058_S+noga 296.2498108 125.302558 467.19706 0.0000009
## M248_S+noga-M058_S+noga 22.5773550 -148.369898 193.52461 1.0000000
## M248_C+lowga-M248_C+higa 82.3507281 -84.037110 248.73857 0.9521875
## M248_C+noga-M248_C+higa -2.4173388 -168.805177 163.97050 1.0000000
## M248_S+higa-M248_C+higa 107.3807518 -59.007086 273.76859 0.6903826
## M248_S+lowga-M248_C+higa 268.6782118 102.290374 435.06605 0.0000072
## M248_S+noga-M248_C+higa -4.9942440 -171.382082 161.39359 1.0000000
## M248_C+noga-M248_C+lowga -84.7680669 -251.155905 81.61977 0.9386889
## M248_S+higa-M248_C+lowga 25.0300237 -141.357814 191.41786 1.0000000
## M248_S+lowga-M248_C+lowga 186.3274837 19.939646 352.71532 0.0124510
## M248_S+noga-M248_C+lowga -87.3449721 -253.732810 79.04287 0.9215674
## M248_S+higa-M248_C+noga 109.7980906 -56.589747 276.18593 0.6533317
## M248_S+lowga-M248_C+noga 271.0955506 104.707713 437.48339 0.0000056
## M248_S+noga-M248_C+noga -2.5769052 -168.964743 163.81093 1.0000000
## M248_S+lowga-M248_S+higa 161.2974600 -5.090378 327.68530 0.0688866
## M248_S+noga-M248_S+higa -112.3749958 -278.762834 54.01284 0.6128258
## M248_S+noga-M248_S+lowga -273.6724558 -440.060294 -107.28462 0.0000043P7 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P7)
stat.test## LA1511_C+lowga LA1511_C+noga LA1511_S+higa LA1511_S+lowga LA1511_S+noga
## "a" "a" "a" "a" "a"
## M058_C+higa M058_C+lowga M058_C+noga M058_S+higa M058_S+lowga
## "a" "a" "a" "a" "a"
## M058_S+noga M248_C+higa M248_C+lowga M248_C+noga M248_S+higa
## "a" "a" "a" "a" "ab"
## M248_S+lowga M248_S+noga LA1511_C+higa
## "b" "a" "a"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowga"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
GA_dataGA_data$All.condition <- factor(GA_data$All.condition, levels = c("C+noga", "C+lowga", "C+higa", "S+noga", "S+lowga", "S+higa"))
GA_data2 <- subset(GA_data, GA_data$Distance.squared < 150)
distance_GA <- ggplot(data = GA_data2, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_GA <- distance_GA + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_GA <- distance_GA + facet_grid(~ Accession, scales = "free_y")
distance_GA <- distance_GA + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_GA <- distance_GA + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
distance_GA <- distance_GA + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 150)
distance_GA <- distance_GA + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_GA <- distance_GA + rremove("legend")
distance_GA
aov(Alpha ~ All.ID2, data = GA_data)## Call:
## aov(formula = Alpha ~ All.ID2, data = GA_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 3.291508 9.020171
## Deg. of Freedom 17 163
##
## Residual standard error: 0.2352413
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Alpha ~ All.ID2, data = GA_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Alpha ~ All.ID2, data = GA_data)
##
## $All.ID2
## diff lwr upr p adj
## LA1511_C+lowga-LA1511_C+higa 0.115909091 -0.248534989 0.480353171 0.9996485
## LA1511_C+noga-LA1511_C+higa -0.074090909 -0.438534989 0.290353171 0.9999994
## LA1511_S+higa-LA1511_C+higa -0.030000000 -0.385661004 0.325661004 1.0000000
## LA1511_S+lowga-LA1511_C+higa -0.118181818 -0.473842822 0.237479186 0.9993817
## LA1511_S+noga-LA1511_C+higa -0.144646465 -0.519546081 0.230253151 0.9962176
## M058_C+higa-LA1511_C+higa 0.113909091 -0.250534989 0.478353171 0.9997202
## M058_C+lowga-LA1511_C+higa 0.230909091 -0.133534989 0.595353171 0.7194684
## M058_C+noga-LA1511_C+higa 0.067909091 -0.296534989 0.432353171 0.9999998
## M058_S+higa-LA1511_C+higa -0.261090909 -0.625534989 0.103353171 0.5038937
## M058_S+lowga-LA1511_C+higa -0.184090909 -0.548534989 0.180353171 0.9429666
## M058_S+noga-LA1511_C+higa -0.121313131 -0.496212747 0.253586485 0.9995600
## M248_C+higa-LA1511_C+higa -0.054090909 -0.418534989 0.310353171 1.0000000
## M248_C+lowga-LA1511_C+higa -0.231090909 -0.595534989 0.133353171 0.7182556
## M248_C+noga-LA1511_C+higa 0.061909091 -0.302534989 0.426353171 1.0000000
## M248_S+higa-LA1511_C+higa -0.020090909 -0.384534989 0.344353171 1.0000000
## M248_S+lowga-LA1511_C+higa -0.267090909 -0.631534989 0.097353171 0.4608954
## M248_S+noga-LA1511_C+higa -0.123090909 -0.487534989 0.241353171 0.9992399
## LA1511_C+noga-LA1511_C+lowga -0.190000000 -0.563020408 0.183020408 0.9387954
## LA1511_S+higa-LA1511_C+lowga -0.145909091 -0.510353171 0.218534989 0.9942560
## LA1511_S+lowga-LA1511_C+lowga -0.234090909 -0.598534989 0.130353171 0.6979856
## LA1511_S+noga-LA1511_C+lowga -0.260555556 -0.643797593 0.122686482 0.6009462
## M058_C+higa-LA1511_C+lowga -0.002000000 -0.375020408 0.371020408 1.0000000
## M058_C+lowga-LA1511_C+lowga 0.115000000 -0.258020408 0.488020408 0.9997666
## M058_C+noga-LA1511_C+lowga -0.048000000 -0.421020408 0.325020408 1.0000000
## M058_S+higa-LA1511_C+lowga -0.377000000 -0.750020408 -0.003979592 0.0445582
## M058_S+lowga-LA1511_C+lowga -0.300000000 -0.673020408 0.073020408 0.2922338
## M058_S+noga-LA1511_C+lowga -0.237222222 -0.620464260 0.146019816 0.7540906
## M248_C+higa-LA1511_C+lowga -0.170000000 -0.543020408 0.203020408 0.9777460
## M248_C+lowga-LA1511_C+lowga -0.347000000 -0.720020408 0.026020408 0.1015069
## M248_C+noga-LA1511_C+lowga -0.054000000 -0.427020408 0.319020408 1.0000000
## M248_S+higa-LA1511_C+lowga -0.136000000 -0.509020408 0.237020408 0.9980531
## M248_S+lowga-LA1511_C+lowga -0.383000000 -0.756020408 -0.009979592 0.0373289
## M248_S+noga-LA1511_C+lowga -0.239000000 -0.612020408 0.134020408 0.7019810
## LA1511_S+higa-LA1511_C+noga 0.044090909 -0.320353171 0.408534989 1.0000000
## LA1511_S+lowga-LA1511_C+noga -0.044090909 -0.408534989 0.320353171 1.0000000
## LA1511_S+noga-LA1511_C+noga -0.070555556 -0.453797593 0.312686482 0.9999999
## M058_C+higa-LA1511_C+noga 0.188000000 -0.185020408 0.561020408 0.9440504
## M058_C+lowga-LA1511_C+noga 0.305000000 -0.068020408 0.678020408 0.2650390
## M058_C+noga-LA1511_C+noga 0.142000000 -0.231020408 0.515020408 0.9967608
## M058_S+higa-LA1511_C+noga -0.187000000 -0.560020408 0.186020408 0.9465538
## M058_S+lowga-LA1511_C+noga -0.110000000 -0.483020408 0.263020408 0.9998714
## M058_S+noga-LA1511_C+noga -0.047222222 -0.430464260 0.336019816 1.0000000
## M248_C+higa-LA1511_C+noga 0.020000000 -0.353020408 0.393020408 1.0000000
## M248_C+lowga-LA1511_C+noga -0.157000000 -0.530020408 0.216020408 0.9901074
## M248_C+noga-LA1511_C+noga 0.136000000 -0.237020408 0.509020408 0.9980531
## M248_S+higa-LA1511_C+noga 0.054000000 -0.319020408 0.427020408 1.0000000
## M248_S+lowga-LA1511_C+noga -0.193000000 -0.566020408 0.180020408 0.9302771
## M248_S+noga-LA1511_C+noga -0.049000000 -0.422020408 0.324020408 1.0000000
## LA1511_S+lowga-LA1511_S+higa -0.088181818 -0.443842822 0.267479186 0.9999887
## LA1511_S+noga-LA1511_S+higa -0.114646465 -0.489546081 0.260253151 0.9997905
## M058_C+higa-LA1511_S+higa 0.143909091 -0.220534989 0.508353171 0.9950779
## M058_C+lowga-LA1511_S+higa 0.260909091 -0.103534989 0.625353171 0.5052095
## M058_C+noga-LA1511_S+higa 0.097909091 -0.266534989 0.462353171 0.9999645
## M058_S+higa-LA1511_S+higa -0.231090909 -0.595534989 0.133353171 0.7182556
## M058_S+lowga-LA1511_S+higa -0.154090909 -0.518534989 0.210353171 0.9896181
## M058_S+noga-LA1511_S+higa -0.091313131 -0.466212747 0.283586485 0.9999913
## M248_C+higa-LA1511_S+higa -0.024090909 -0.388534989 0.340353171 1.0000000
## M248_C+lowga-LA1511_S+higa -0.201090909 -0.565534989 0.163353171 0.8848352
## M248_C+noga-LA1511_S+higa 0.091909091 -0.272534989 0.456353171 0.9999856
## M248_S+higa-LA1511_S+higa 0.009909091 -0.354534989 0.374353171 1.0000000
## M248_S+lowga-LA1511_S+higa -0.237090909 -0.601534989 0.127353171 0.6772747
## M248_S+noga-LA1511_S+higa -0.093090909 -0.457534989 0.271353171 0.9999827
## LA1511_S+noga-LA1511_S+lowga -0.026464646 -0.401364262 0.348434970 1.0000000
## M058_C+higa-LA1511_S+lowga 0.232090909 -0.132353171 0.596534989 0.7115519
## M058_C+lowga-LA1511_S+lowga 0.349090909 -0.015353171 0.713534989 0.0774260
## M058_C+noga-LA1511_S+lowga 0.186090909 -0.178353171 0.550534989 0.9375114
## M058_S+higa-LA1511_S+lowga -0.142909091 -0.507353171 0.221534989 0.9954505
## M058_S+lowga-LA1511_S+lowga -0.065909091 -0.430353171 0.298534989 0.9999999
## M058_S+noga-LA1511_S+lowga -0.003131313 -0.378030929 0.371768303 1.0000000
## M248_C+higa-LA1511_S+lowga 0.064090909 -0.300353171 0.428534989 0.9999999
## M248_C+lowga-LA1511_S+lowga -0.112909091 -0.477353171 0.251534989 0.9997509
## M248_C+noga-LA1511_S+lowga 0.180090909 -0.184353171 0.544534989 0.9528453
## M248_S+higa-LA1511_S+lowga 0.098090909 -0.266353171 0.462534989 0.9999636
## M248_S+lowga-LA1511_S+lowga -0.148909091 -0.513353171 0.215534989 0.9928116
## M248_S+noga-LA1511_S+lowga -0.004909091 -0.369353171 0.359534989 1.0000000
## M058_C+higa-LA1511_S+noga 0.258555556 -0.124686482 0.641797593 0.6147425
## M058_C+lowga-LA1511_S+noga 0.375555556 -0.007686482 0.758797593 0.0617933
## M058_C+noga-LA1511_S+noga 0.212555556 -0.170686482 0.595797593 0.8803936
## M058_S+higa-LA1511_S+noga -0.116444444 -0.499686482 0.266797593 0.9998077
## M058_S+lowga-LA1511_S+noga -0.039444444 -0.422686482 0.343797593 1.0000000
## M058_S+noga-LA1511_S+noga 0.023333333 -0.369864701 0.416531368 1.0000000
## M248_C+higa-LA1511_S+noga 0.090555556 -0.292686482 0.473797593 0.9999944
## M248_C+lowga-LA1511_S+noga -0.086444444 -0.469686482 0.296797593 0.9999972
## M248_C+noga-LA1511_S+noga 0.206555556 -0.176686482 0.589797593 0.9035089
## M248_S+higa-LA1511_S+noga 0.124555556 -0.258686482 0.507797593 0.9995345
## M248_S+lowga-LA1511_S+noga -0.122444444 -0.505686482 0.260797593 0.9996270
## M248_S+noga-LA1511_S+noga 0.021555556 -0.361686482 0.404797593 1.0000000
## M058_C+lowga-M058_C+higa 0.117000000 -0.256020408 0.490020408 0.9997070
## M058_C+noga-M058_C+higa -0.046000000 -0.419020408 0.327020408 1.0000000
## M058_S+higa-M058_C+higa -0.375000000 -0.748020408 -0.001979592 0.0472251
## M058_S+lowga-M058_C+higa -0.298000000 -0.671020408 0.075020408 0.3035597
## M058_S+noga-M058_C+higa -0.235222222 -0.618464260 0.148019816 0.7660109
## M248_C+higa-M058_C+higa -0.168000000 -0.541020408 0.205020408 0.9801874
## M248_C+lowga-M058_C+higa -0.345000000 -0.718020408 0.028020408 0.1068210
## M248_C+noga-M058_C+higa -0.052000000 -0.425020408 0.321020408 1.0000000
## M248_S+higa-M058_C+higa -0.134000000 -0.507020408 0.239020408 0.9983712
## M248_S+lowga-M058_C+higa -0.381000000 -0.754020408 -0.007979592 0.0396153
## M248_S+noga-M058_C+higa -0.237000000 -0.610020408 0.136020408 0.7151781
## M058_C+noga-M058_C+lowga -0.163000000 -0.536020408 0.210020408 0.9853773
## M058_S+higa-M058_C+lowga -0.492000000 -0.865020408 -0.118979592 0.0008261
## M058_S+lowga-M058_C+lowga -0.415000000 -0.788020408 -0.041979592 0.0136289
## M058_S+noga-M058_C+lowga -0.352222222 -0.735464260 0.031019816 0.1128432
## M248_C+higa-M058_C+lowga -0.285000000 -0.658020408 0.088020408 0.3829306
## M248_C+lowga-M058_C+lowga -0.462000000 -0.835020408 -0.088979592 0.0026084
## M248_C+noga-M058_C+lowga -0.169000000 -0.542020408 0.204020408 0.9789944
## M248_S+higa-M058_C+lowga -0.251000000 -0.624020408 0.122020408 0.6194016
## M248_S+lowga-M058_C+lowga -0.498000000 -0.871020408 -0.124979592 0.0006511
## M248_S+noga-M058_C+lowga -0.354000000 -0.727020408 0.019020408 0.0845724
## M058_S+higa-M058_C+noga -0.329000000 -0.702020408 0.044020408 0.1577198
## M058_S+lowga-M058_C+noga -0.252000000 -0.625020408 0.121020408 0.6123338
## M058_S+noga-M058_C+noga -0.189222222 -0.572464260 0.194019816 0.9531898
## M248_C+higa-M058_C+noga -0.122000000 -0.495020408 0.251020408 0.9994952
## M248_C+lowga-M058_C+noga -0.299000000 -0.672020408 0.074020408 0.2978653
## M248_C+noga-M058_C+noga -0.006000000 -0.379020408 0.367020408 1.0000000
## M248_S+higa-M058_C+noga -0.088000000 -0.461020408 0.285020408 0.9999946
## M248_S+lowga-M058_C+noga -0.335000000 -0.708020408 0.038020408 0.1368144
## M248_S+noga-M058_C+noga -0.191000000 -0.564020408 0.182020408 0.9360417
## M058_S+lowga-M058_S+higa 0.077000000 -0.296020408 0.450020408 0.9999993
## M058_S+noga-M058_S+higa 0.139777778 -0.243464260 0.523019816 0.9980445
## M248_C+higa-M058_S+higa 0.207000000 -0.166020408 0.580020408 0.8799129
## M248_C+lowga-M058_S+higa 0.030000000 -0.343020408 0.403020408 1.0000000
## M248_C+noga-M058_S+higa 0.323000000 -0.050020408 0.696020408 0.1809386
## M248_S+higa-M058_S+higa 0.241000000 -0.132020408 0.614020408 0.6885914
## M248_S+lowga-M058_S+higa -0.006000000 -0.379020408 0.367020408 1.0000000
## M248_S+noga-M058_S+higa 0.138000000 -0.235020408 0.511020408 0.9976831
## M058_S+noga-M058_S+lowga 0.062777778 -0.320464260 0.446019816 1.0000000
## M248_C+higa-M058_S+lowga 0.130000000 -0.243020408 0.503020408 0.9988758
## M248_C+lowga-M058_S+lowga -0.047000000 -0.420020408 0.326020408 1.0000000
## M248_C+noga-M058_S+lowga 0.246000000 -0.127020408 0.619020408 0.6543948
## M248_S+higa-M058_S+lowga 0.164000000 -0.209020408 0.537020408 0.9844374
## M248_S+lowga-M058_S+lowga -0.083000000 -0.456020408 0.290020408 0.9999977
## M248_S+noga-M058_S+lowga 0.061000000 -0.312020408 0.434020408 1.0000000
## M248_C+higa-M058_S+noga 0.067222222 -0.316019816 0.450464260 0.9999999
## M248_C+lowga-M058_S+noga -0.109777778 -0.493019816 0.273464260 0.9999135
## M248_C+noga-M058_S+noga 0.183222222 -0.200019816 0.566464260 0.9649741
## M248_S+higa-M058_S+noga 0.101222222 -0.282019816 0.484464260 0.9999721
## M248_S+lowga-M058_S+noga -0.145777778 -0.529019816 0.237464260 0.9967899
## M248_S+noga-M058_S+noga -0.001777778 -0.385019816 0.381464260 1.0000000
## M248_C+lowga-M248_C+higa -0.177000000 -0.550020408 0.196020408 0.9673239
## M248_C+noga-M248_C+higa 0.116000000 -0.257020408 0.489020408 0.9997383
## M248_S+higa-M248_C+higa 0.034000000 -0.339020408 0.407020408 1.0000000
## M248_S+lowga-M248_C+higa -0.213000000 -0.586020408 0.160020408 0.8528584
## M248_S+noga-M248_C+higa -0.069000000 -0.442020408 0.304020408 0.9999999
## M248_C+noga-M248_C+lowga 0.293000000 -0.080020408 0.666020408 0.3329488
## M248_S+higa-M248_C+lowga 0.211000000 -0.162020408 0.584020408 0.8622379
## M248_S+lowga-M248_C+lowga -0.036000000 -0.409020408 0.337020408 1.0000000
## M248_S+noga-M248_C+lowga 0.108000000 -0.265020408 0.481020408 0.9998998
## M248_S+higa-M248_C+noga -0.082000000 -0.455020408 0.291020408 0.9999981
## M248_S+lowga-M248_C+noga -0.329000000 -0.702020408 0.044020408 0.1577198
## M248_S+noga-M248_C+noga -0.185000000 -0.558020408 0.188020408 0.9513180
## M248_S+lowga-M248_S+higa -0.247000000 -0.620020408 0.126020408 0.6474504
## M248_S+noga-M248_S+higa -0.103000000 -0.476020408 0.270020408 0.9999479
## M248_S+noga-M248_S+lowga 0.144000000 -0.229020408 0.517020408 0.9961938P8 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P8)
stat.test## LA1511_C+lowga LA1511_C+noga LA1511_S+higa LA1511_S+lowga LA1511_S+noga
## "ab" "abc" "abc" "abc" "abc"
## M058_C+higa M058_C+lowga M058_C+noga M058_S+higa M058_S+lowga
## "ab" "a" "abc" "c" "bc"
## M058_S+noga M248_C+higa M248_C+lowga M248_C+noga M248_S+higa
## "abc" "abc" "bc" "abc" "abc"
## M248_S+lowga M248_S+noga LA1511_C+higa
## "c" "abc" "abc"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowga"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
GA_dataGA_data$All.condition <- factor(GA_data$All.condition, levels = c("C+noga", "C+lowga", "C+higa", "S+noga", "S+lowga", "S+higa"))
#GA_data2 <- subset(GA_data, GA_data$Distance.squared < 150)
distance_GA <- ggplot(data = GA_data, mapping = aes(x = All.condition, y = Alpha, colour = All.condition))
distance_GA <- distance_GA + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_GA <- distance_GA + facet_grid(~ Accession, scales = "free_y")
distance_GA <- distance_GA + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_GA <- distance_GA + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
distance_GA <- distance_GA + ylab("Alpha") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 1.2)
distance_GA <- distance_GA + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_GA <- distance_GA + rremove("legend")
distance_GA
list.files(pattern=".csv")## [1] "ABA-only.csv"
## [2] "ACC-only-d5excluded.csv"
## [3] "ACC-only.csv"
## [4] "cyto-only.csv"
## [5] "GA-only-d5excluded.csv"
## [6] "GA-only.csv"
## [7] "IAA-only-d5excluded.csv"
## [8] "IAA-only.csv"
## [9] "point_similarity_maryamModified.csv"
## [10] "point_similarity_maryamModified_control_Removed.csv"Cyto_data <- read.csv("cyto-only.csv")
Cyto_dataCyto_data$All.condition<-paste(Cyto_data$Condition1,Cyto_data$Condition2, sep="+")
Cyto_dataCyto_data$All.ID2<-paste(Cyto_data$Accession,Cyto_data$All.condition,sep="_")
Cyto_dataaov(Distance.squared ~ All.ID2, data = Cyto_data)## Call:
## aov(formula = Distance.squared ~ All.ID2, data = Cyto_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 21186.47 48386.23
## Deg. of Freedom 17 144
##
## Residual standard error: 18.33073
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Distance.squared ~ All.ID2, data = Cyto_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Distance.squared ~ All.ID2, data = Cyto_data)
##
## $All.ID2
## diff lwr upr
## LA1511_C+lowcyto-LA1511_C+hicyto 0.055413500 -29.0734286 29.1842556
## LA1511_C+nocyto-LA1511_C+hicyto 3.348439733 -30.2866499 36.9835294
## LA1511_S+hicyto-LA1511_C+hicyto -0.005791700 -29.1346338 29.1230504
## LA1511_S+lowcyto-LA1511_C+hicyto 0.021479733 -29.9055606 29.9485201
## LA1511_S+nocyto-LA1511_C+hicyto 17.097080700 -12.0317614 46.2259228
## M058_C+hicyto-LA1511_C+hicyto 0.008759525 -30.8870431 30.9045622
## M058_C+lowcyto-LA1511_C+hicyto 0.110933600 -29.0179085 29.2397757
## M058_C+nocyto-LA1511_C+hicyto 4.405077400 -24.7237647 33.5339195
## M058_S+hicyto-LA1511_C+hicyto 0.017204775 -30.8785979 30.9130074
## M058_S+lowcyto-LA1511_C+hicyto 0.039328100 -29.0895140 29.1681702
## M058_S+nocyto-LA1511_C+hicyto 2.593774900 -35.9400611 41.1276109
## M248_C+hicyto-LA1511_C+hicyto 0.019499000 -29.1093431 29.1483411
## M248_C+lowcyto-LA1511_C+hicyto 0.130470000 -28.9983721 29.2593121
## M248_C+nocyto-LA1511_C+hicyto 29.712098800 0.5832567 58.8409409
## M248_S+hicyto-LA1511_C+hicyto 0.001647275 -30.8941554 30.8974499
## M248_S+lowcyto-LA1511_C+hicyto 0.148166178 -29.7788741 30.0752065
## M248_S+nocyto-LA1511_C+hicyto 38.032189300 8.9033472 67.1610314
## LA1511_C+nocyto-LA1511_C+lowcyto 3.293026233 -30.3420634 36.9281159
## LA1511_S+hicyto-LA1511_C+lowcyto -0.061205200 -29.1900473 29.0676369
## LA1511_S+lowcyto-LA1511_C+lowcyto -0.033933767 -29.9609741 29.8931066
## LA1511_S+nocyto-LA1511_C+lowcyto 17.041667200 -12.0871749 46.1705093
## M058_C+hicyto-LA1511_C+lowcyto -0.046653975 -30.9424566 30.8491487
## M058_C+lowcyto-LA1511_C+lowcyto 0.055520100 -29.0733220 29.1843622
## M058_C+nocyto-LA1511_C+lowcyto 4.349663900 -24.7791782 33.4785060
## M058_S+hicyto-LA1511_C+lowcyto -0.038208725 -30.9340114 30.8575939
## M058_S+lowcyto-LA1511_C+lowcyto -0.016085400 -29.1449275 29.1127567
## M058_S+nocyto-LA1511_C+lowcyto 2.538361400 -35.9954746 41.0721974
## M248_C+hicyto-LA1511_C+lowcyto -0.035914500 -29.1647566 29.0929276
## M248_C+lowcyto-LA1511_C+lowcyto 0.075056500 -29.0537856 29.2038986
## M248_C+nocyto-LA1511_C+lowcyto 29.656685300 0.5278432 58.7855274
## M248_S+hicyto-LA1511_C+lowcyto -0.053766225 -30.9495689 30.8420364
## M248_S+lowcyto-LA1511_C+lowcyto 0.092752678 -29.8342876 30.0197930
## M248_S+nocyto-LA1511_C+lowcyto 37.976775800 8.8479337 67.1056179
## LA1511_S+hicyto-LA1511_C+nocyto -3.354231433 -36.9893211 30.2808582
## LA1511_S+lowcyto-LA1511_C+nocyto -3.326960000 -37.6556296 31.0017096
## LA1511_S+nocyto-LA1511_C+nocyto 13.748640967 -19.8864487 47.3837306
## M058_C+hicyto-LA1511_C+nocyto -3.339680208 -38.5160989 31.8367385
## M058_C+lowcyto-LA1511_C+nocyto -3.237506133 -36.8725958 30.3975835
## M058_C+nocyto-LA1511_C+nocyto 1.056637667 -32.5784520 34.6917273
## M058_S+hicyto-LA1511_C+nocyto -3.331234958 -38.5076537 31.8451838
## M058_S+lowcyto-LA1511_C+nocyto -3.309111633 -36.9442013 30.3259780
## M058_S+nocyto-LA1511_C+nocyto -0.754664833 -42.7985269 41.2891972
## M248_C+hicyto-LA1511_C+nocyto -3.328940733 -36.9640304 30.3061489
## M248_C+lowcyto-LA1511_C+nocyto -3.217969733 -36.8530594 30.4171199
## M248_C+nocyto-LA1511_C+nocyto 26.363659067 -7.2714306 59.9987487
## M248_S+hicyto-LA1511_C+nocyto -3.346792458 -38.5232112 31.8296263
## M248_S+lowcyto-LA1511_C+nocyto -3.200273556 -37.5289431 31.1283960
## M248_S+nocyto-LA1511_C+nocyto 34.683749567 1.0486599 68.3188392
## LA1511_S+lowcyto-LA1511_S+hicyto 0.027271433 -29.8997689 29.9543118
## LA1511_S+nocyto-LA1511_S+hicyto 17.102872400 -12.0259697 46.2317145
## M058_C+hicyto-LA1511_S+hicyto 0.014551225 -30.8812514 30.9103539
## M058_C+lowcyto-LA1511_S+hicyto 0.116725300 -29.0121168 29.2455674
## M058_C+nocyto-LA1511_S+hicyto 4.410869100 -24.7179730 33.5397112
## M058_S+hicyto-LA1511_S+hicyto 0.022996475 -30.8728062 30.9187991
## M058_S+lowcyto-LA1511_S+hicyto 0.045119800 -29.0837223 29.1739619
## M058_S+nocyto-LA1511_S+hicyto 2.599566600 -35.9342694 41.1334026
## M248_C+hicyto-LA1511_S+hicyto 0.025290700 -29.1035514 29.1541328
## M248_C+lowcyto-LA1511_S+hicyto 0.136261700 -28.9925804 29.2651038
## M248_C+nocyto-LA1511_S+hicyto 29.717890500 0.5890484 58.8467326
## M248_S+hicyto-LA1511_S+hicyto 0.007438975 -30.8883637 30.9032416
## M248_S+lowcyto-LA1511_S+hicyto 0.153957878 -29.7730824 30.0809982
## M248_S+nocyto-LA1511_S+hicyto 38.037981000 8.9091389 67.1668231
## LA1511_S+nocyto-LA1511_S+lowcyto 17.075600967 -12.8514394 47.0026413
## M058_C+hicyto-LA1511_S+lowcyto -0.012720208 -31.6621898 31.6367493
## M058_C+lowcyto-LA1511_S+lowcyto 0.089453867 -29.8375865 30.0164942
## M058_C+nocyto-LA1511_S+lowcyto 4.383597667 -25.5434427 34.3106380
## M058_S+hicyto-LA1511_S+lowcyto -0.004274958 -31.6537445 31.6451946
## M058_S+lowcyto-LA1511_S+lowcyto 0.017848367 -29.9091920 29.9448887
## M058_S+nocyto-LA1511_S+lowcyto 2.572295167 -36.5684103 41.7130006
## M248_C+hicyto-LA1511_S+lowcyto -0.001980733 -29.9290211 29.9250596
## M248_C+lowcyto-LA1511_S+lowcyto 0.108990267 -29.8180501 30.0360306
## M248_C+nocyto-LA1511_S+lowcyto 29.690619067 -0.2364213 59.6176594
## M248_S+hicyto-LA1511_S+lowcyto -0.019832458 -31.6693020 31.6296371
## M248_S+lowcyto-LA1511_S+lowcyto 0.126686444 -30.5778091 30.8311820
## M248_S+nocyto-LA1511_S+lowcyto 38.010709567 8.0836692 67.9377499
## M058_C+hicyto-LA1511_S+nocyto -17.088321175 -47.9841238 13.8074815
## M058_C+lowcyto-LA1511_S+nocyto -16.986147100 -46.1149892 12.1426950
## M058_C+nocyto-LA1511_S+nocyto -12.692003300 -41.8208454 16.4368388
## M058_S+hicyto-LA1511_S+nocyto -17.079875925 -47.9756786 13.8159267
## M058_S+lowcyto-LA1511_S+nocyto -17.057752600 -46.1865947 12.0710895
## M058_S+nocyto-LA1511_S+nocyto -14.503305800 -53.0371418 24.0305302
## M248_C+hicyto-LA1511_S+nocyto -17.077581700 -46.2064238 12.0512604
## M248_C+lowcyto-LA1511_S+nocyto -16.966610700 -46.0954528 12.1622314
## M248_C+nocyto-LA1511_S+nocyto 12.615018100 -16.5138240 41.7438602
## M248_S+hicyto-LA1511_S+nocyto -17.095433425 -47.9912361 13.8003692
## M248_S+lowcyto-LA1511_S+nocyto -16.948914522 -46.8759548 12.9781258
## M248_S+nocyto-LA1511_S+nocyto 20.935108600 -8.1937335 50.0639507
## M058_C+lowcyto-M058_C+hicyto 0.102174075 -30.7936286 30.9979767
## M058_C+nocyto-M058_C+hicyto 4.396317875 -26.4994848 35.2921205
## M058_S+hicyto-M058_C+hicyto 0.008445250 -32.5585902 32.5754807
## M058_S+lowcyto-M058_C+hicyto 0.030568575 -30.8652341 30.9263712
## M058_S+nocyto-M058_C+hicyto 2.585015375 -37.3012943 42.4713251
## M248_C+hicyto-M058_C+hicyto 0.010739475 -30.8850632 30.9065421
## M248_C+lowcyto-M058_C+hicyto 0.121710475 -30.7740922 31.0175131
## M248_C+nocyto-M058_C+hicyto 29.703339275 -1.1924634 60.5991419
## M248_S+hicyto-M058_C+hicyto -0.007112250 -32.5741477 32.5599232
## M248_S+lowcyto-M058_C+hicyto 0.139406653 -31.5100629 31.7888762
## M248_S+nocyto-M058_C+hicyto 38.023429775 7.1276271 68.9192324
## M058_C+nocyto-M058_C+lowcyto 4.294143800 -24.8346983 33.4229859
## M058_S+hicyto-M058_C+lowcyto -0.093728825 -30.9895315 30.8020738
## M058_S+lowcyto-M058_C+lowcyto -0.071605500 -29.2004476 29.0572366
## M058_S+nocyto-M058_C+lowcyto 2.482841300 -36.0509947 41.0166773
## M248_C+hicyto-M058_C+lowcyto -0.091434600 -29.2202767 29.0374075
## M248_C+lowcyto-M058_C+lowcyto 0.019536400 -29.1093057 29.1483785
## M248_C+nocyto-M058_C+lowcyto 29.601165200 0.4723231 58.7300073
## M248_S+hicyto-M058_C+lowcyto -0.109286325 -31.0050890 30.7865163
## M248_S+lowcyto-M058_C+lowcyto 0.037232578 -29.8898077 29.9642729
## M248_S+nocyto-M058_C+lowcyto 37.921255700 8.7924136 67.0500978
## M058_S+hicyto-M058_C+nocyto -4.387872625 -35.2836753 26.5079300
## M058_S+lowcyto-M058_C+nocyto -4.365749300 -33.4945914 24.7630928
## M058_S+nocyto-M058_C+nocyto -1.811302500 -40.3451385 36.7225335
## M248_C+hicyto-M058_C+nocyto -4.385578400 -33.5144205 24.7432637
## M248_C+lowcyto-M058_C+nocyto -4.274607400 -33.4034495 24.8542347
## M248_C+nocyto-M058_C+nocyto 25.307021400 -3.8218207 54.4358635
## M248_S+hicyto-M058_C+nocyto -4.403430125 -35.2992328 26.4923725
## M248_S+lowcyto-M058_C+nocyto -4.256911222 -34.1839515 25.6701291
## M248_S+nocyto-M058_C+nocyto 33.627111900 4.4982698 62.7559540
## M058_S+lowcyto-M058_S+hicyto 0.022123325 -30.8736793 30.9179260
## M058_S+nocyto-M058_S+hicyto 2.576570125 -37.3097396 42.4628798
## M248_C+hicyto-M058_S+hicyto 0.002294225 -30.8935084 30.8980969
## M248_C+lowcyto-M058_S+hicyto 0.113265225 -30.7825374 31.0090679
## M248_C+nocyto-M058_S+hicyto 29.694894025 -1.2009086 60.5906967
## M248_S+hicyto-M058_S+hicyto -0.015557500 -32.5825930 32.5514780
## M248_S+lowcyto-M058_S+hicyto 0.130961403 -31.5185081 31.7804309
## M248_S+nocyto-M058_S+hicyto 38.014984525 7.1191819 68.9107872
## M058_S+nocyto-M058_S+lowcyto 2.554446800 -35.9793892 41.0882828
## M248_C+hicyto-M058_S+lowcyto -0.019829100 -29.1486712 29.1090130
## M248_C+lowcyto-M058_S+lowcyto 0.091141900 -29.0377002 29.2199840
## M248_C+nocyto-M058_S+lowcyto 29.672770700 0.5439286 58.8016128
## M248_S+hicyto-M058_S+lowcyto -0.037680825 -30.9334835 30.8581218
## M248_S+lowcyto-M058_S+lowcyto 0.108838078 -29.8182022 30.0358784
## M248_S+nocyto-M058_S+lowcyto 37.992861200 8.8640191 67.1217033
## M248_C+hicyto-M058_S+nocyto -2.574275900 -41.1081119 35.9595601
## M248_C+lowcyto-M058_S+nocyto -2.463304900 -40.9971409 36.0705311
## M248_C+nocyto-M058_S+nocyto 27.118323900 -11.4155121 65.6521599
## M248_S+hicyto-M058_S+nocyto -2.592127625 -42.4784373 37.2941821
## M248_S+lowcyto-M058_S+nocyto -2.445608722 -41.5863142 36.6950967
## M248_S+nocyto-M058_S+nocyto 35.438414400 -3.0954216 73.9722504
## M248_C+lowcyto-M248_C+hicyto 0.110971000 -29.0178711 29.2398131
## M248_C+nocyto-M248_C+hicyto 29.692599800 0.5637577 58.8214419
## M248_S+hicyto-M248_C+hicyto -0.017851725 -30.9136544 30.8779509
## M248_S+lowcyto-M248_C+hicyto 0.128667178 -29.7983731 30.0557075
## M248_S+nocyto-M248_C+hicyto 38.012690300 8.8838482 67.1415324
## M248_C+nocyto-M248_C+lowcyto 29.581628800 0.4527867 58.7104709
## M248_S+hicyto-M248_C+lowcyto -0.128822725 -31.0246254 30.7669799
## M248_S+lowcyto-M248_C+lowcyto 0.017696178 -29.9093441 29.9447365
## M248_S+nocyto-M248_C+lowcyto 37.901719300 8.7728772 67.0305614
## M248_S+hicyto-M248_C+nocyto -29.710451525 -60.6062542 1.1853511
## M248_S+lowcyto-M248_C+nocyto -29.563932622 -59.4909729 0.3631077
## M248_S+nocyto-M248_C+nocyto 8.320090500 -20.8087516 37.4489326
## M248_S+lowcyto-M248_S+hicyto 0.146518903 -31.5029506 31.7959884
## M248_S+nocyto-M248_S+hicyto 38.030542025 7.1347394 68.9263447
## M248_S+nocyto-M248_S+lowcyto 37.884023122 7.9569828 67.8110634
## p adj
## LA1511_C+lowcyto-LA1511_C+hicyto 1.0000000
## LA1511_C+nocyto-LA1511_C+hicyto 1.0000000
## LA1511_S+hicyto-LA1511_C+hicyto 1.0000000
## LA1511_S+lowcyto-LA1511_C+hicyto 1.0000000
## LA1511_S+nocyto-LA1511_C+hicyto 0.8198603
## M058_C+hicyto-LA1511_C+hicyto 1.0000000
## M058_C+lowcyto-LA1511_C+hicyto 1.0000000
## M058_C+nocyto-LA1511_C+hicyto 1.0000000
## M058_S+hicyto-LA1511_C+hicyto 1.0000000
## M058_S+lowcyto-LA1511_C+hicyto 1.0000000
## M058_S+nocyto-LA1511_C+hicyto 1.0000000
## M248_C+hicyto-LA1511_C+hicyto 1.0000000
## M248_C+lowcyto-LA1511_C+hicyto 1.0000000
## M248_C+nocyto-LA1511_C+hicyto 0.0402759
## M248_S+hicyto-LA1511_C+hicyto 1.0000000
## M248_S+lowcyto-LA1511_C+hicyto 1.0000000
## M248_S+nocyto-LA1511_C+hicyto 0.0010427
## LA1511_C+nocyto-LA1511_C+lowcyto 1.0000000
## LA1511_S+hicyto-LA1511_C+lowcyto 1.0000000
## LA1511_S+lowcyto-LA1511_C+lowcyto 1.0000000
## LA1511_S+nocyto-LA1511_C+lowcyto 0.8236247
## M058_C+hicyto-LA1511_C+lowcyto 1.0000000
## M058_C+lowcyto-LA1511_C+lowcyto 1.0000000
## M058_C+nocyto-LA1511_C+lowcyto 1.0000000
## M058_S+hicyto-LA1511_C+lowcyto 1.0000000
## M058_S+lowcyto-LA1511_C+lowcyto 1.0000000
## M058_S+nocyto-LA1511_C+lowcyto 1.0000000
## M248_C+hicyto-LA1511_C+lowcyto 1.0000000
## M248_C+lowcyto-LA1511_C+lowcyto 1.0000000
## M248_C+nocyto-LA1511_C+lowcyto 0.0411226
## M248_S+hicyto-LA1511_C+lowcyto 1.0000000
## M248_S+lowcyto-LA1511_C+lowcyto 1.0000000
## M248_S+nocyto-LA1511_C+lowcyto 0.0010717
## LA1511_S+hicyto-LA1511_C+nocyto 1.0000000
## LA1511_S+lowcyto-LA1511_C+nocyto 1.0000000
## LA1511_S+nocyto-LA1511_C+nocyto 0.9924837
## M058_C+hicyto-LA1511_C+nocyto 1.0000000
## M058_C+lowcyto-LA1511_C+nocyto 1.0000000
## M058_C+nocyto-LA1511_C+nocyto 1.0000000
## M058_S+hicyto-LA1511_C+nocyto 1.0000000
## M058_S+lowcyto-LA1511_C+nocyto 1.0000000
## M058_S+nocyto-LA1511_C+nocyto 1.0000000
## M248_C+hicyto-LA1511_C+nocyto 1.0000000
## M248_C+lowcyto-LA1511_C+nocyto 1.0000000
## M248_C+nocyto-LA1511_C+nocyto 0.3342755
## M248_S+hicyto-LA1511_C+nocyto 1.0000000
## M248_S+lowcyto-LA1511_C+nocyto 1.0000000
## M248_S+nocyto-LA1511_C+nocyto 0.0356121
## LA1511_S+lowcyto-LA1511_S+hicyto 1.0000000
## LA1511_S+nocyto-LA1511_S+hicyto 0.8194644
## M058_C+hicyto-LA1511_S+hicyto 1.0000000
## M058_C+lowcyto-LA1511_S+hicyto 1.0000000
## M058_C+nocyto-LA1511_S+hicyto 1.0000000
## M058_S+hicyto-LA1511_S+hicyto 1.0000000
## M058_S+lowcyto-LA1511_S+hicyto 1.0000000
## M058_S+nocyto-LA1511_S+hicyto 1.0000000
## M248_C+hicyto-LA1511_S+hicyto 1.0000000
## M248_C+lowcyto-LA1511_S+hicyto 1.0000000
## M248_C+nocyto-LA1511_S+hicyto 0.0401883
## M248_S+hicyto-LA1511_S+hicyto 1.0000000
## M248_S+lowcyto-LA1511_S+hicyto 1.0000000
## M248_S+nocyto-LA1511_S+hicyto 0.0010397
## LA1511_S+nocyto-LA1511_S+lowcyto 0.8508610
## M058_C+hicyto-LA1511_S+lowcyto 1.0000000
## M058_C+lowcyto-LA1511_S+lowcyto 1.0000000
## M058_C+nocyto-LA1511_S+lowcyto 1.0000000
## M058_S+hicyto-LA1511_S+lowcyto 1.0000000
## M058_S+lowcyto-LA1511_S+lowcyto 1.0000000
## M058_S+nocyto-LA1511_S+lowcyto 1.0000000
## M248_C+hicyto-LA1511_S+lowcyto 1.0000000
## M248_C+lowcyto-LA1511_S+lowcyto 1.0000000
## M248_C+nocyto-LA1511_S+lowcyto 0.0543623
## M248_S+hicyto-LA1511_S+lowcyto 1.0000000
## M248_S+lowcyto-LA1511_S+lowcyto 1.0000000
## M248_S+nocyto-LA1511_S+lowcyto 0.0017284
## M058_C+hicyto-LA1511_S+nocyto 0.8803320
## M058_C+lowcyto-LA1511_S+nocyto 0.8273544
## M058_C+nocyto-LA1511_S+nocyto 0.9852784
## M058_S+hicyto-LA1511_S+nocyto 0.8807623
## M058_S+lowcyto-LA1511_S+nocyto 0.8225363
## M058_S+nocyto-LA1511_S+nocyto 0.9970312
## M248_C+hicyto-LA1511_S+nocyto 0.8211897
## M248_C+lowcyto-LA1511_S+nocyto 0.8286567
## M248_C+nocyto-LA1511_S+nocyto 0.9861659
## M248_S+hicyto-LA1511_S+nocyto 0.8799688
## M248_S+lowcyto-LA1511_S+nocyto 0.8583489
## M248_S+nocyto-LA1511_S+nocyto 0.4944611
## M058_C+lowcyto-M058_C+hicyto 1.0000000
## M058_C+nocyto-M058_C+hicyto 1.0000000
## M058_S+hicyto-M058_C+hicyto 1.0000000
## M058_S+lowcyto-M058_C+hicyto 1.0000000
## M058_S+nocyto-M058_C+hicyto 1.0000000
## M248_C+hicyto-M058_C+hicyto 1.0000000
## M248_C+lowcyto-M058_C+hicyto 1.0000000
## M248_C+nocyto-M058_C+hicyto 0.0745445
## M248_S+hicyto-M058_C+hicyto 1.0000000
## M248_S+lowcyto-M058_C+hicyto 1.0000000
## M248_S+nocyto-M058_C+hicyto 0.0029815
## M058_C+nocyto-M058_C+lowcyto 1.0000000
## M058_S+hicyto-M058_C+lowcyto 1.0000000
## M058_S+lowcyto-M058_C+lowcyto 1.0000000
## M058_S+nocyto-M058_C+lowcyto 1.0000000
## M248_C+hicyto-M058_C+lowcyto 1.0000000
## M248_C+lowcyto-M058_C+lowcyto 1.0000000
## M248_C+nocyto-M058_C+lowcyto 0.0419866
## M248_S+hicyto-M058_C+lowcyto 1.0000000
## M248_S+lowcyto-M058_C+lowcyto 1.0000000
## M248_S+nocyto-M058_C+lowcyto 0.0011014
## M058_S+hicyto-M058_C+nocyto 1.0000000
## M058_S+lowcyto-M058_C+nocyto 1.0000000
## M058_S+nocyto-M058_C+nocyto 1.0000000
## M248_C+hicyto-M058_C+nocyto 1.0000000
## M248_C+lowcyto-M058_C+nocyto 1.0000000
## M248_C+nocyto-M058_C+nocyto 0.1755140
## M248_S+hicyto-M058_C+nocyto 1.0000000
## M248_S+lowcyto-M058_C+nocyto 1.0000000
## M248_S+nocyto-M058_C+nocyto 0.0081565
## M058_S+lowcyto-M058_S+hicyto 1.0000000
## M058_S+nocyto-M058_S+hicyto 1.0000000
## M248_C+hicyto-M058_S+hicyto 1.0000000
## M248_C+lowcyto-M058_S+hicyto 1.0000000
## M248_C+nocyto-M058_S+hicyto 0.0747493
## M248_S+hicyto-M058_S+hicyto 1.0000000
## M248_S+lowcyto-M058_S+hicyto 1.0000000
## M248_S+nocyto-M058_S+hicyto 0.0029926
## M058_S+nocyto-M058_S+lowcyto 1.0000000
## M248_C+hicyto-M058_S+lowcyto 1.0000000
## M248_C+lowcyto-M058_S+lowcyto 1.0000000
## M248_C+nocyto-M058_S+lowcyto 0.0408753
## M248_S+hicyto-M058_S+lowcyto 1.0000000
## M248_S+lowcyto-M058_S+lowcyto 1.0000000
## M248_S+nocyto-M058_S+lowcyto 0.0010632
## M248_C+hicyto-M058_S+nocyto 1.0000000
## M248_C+lowcyto-M058_S+nocyto 1.0000000
## M248_C+nocyto-M058_S+nocyto 0.5339001
## M248_S+hicyto-M058_S+nocyto 1.0000000
## M248_S+lowcyto-M058_S+nocyto 1.0000000
## M248_S+nocyto-M058_S+nocyto 0.1117065
## M248_C+lowcyto-M248_C+hicyto 1.0000000
## M248_C+nocyto-M248_C+hicyto 0.0405721
## M248_S+hicyto-M248_C+hicyto 1.0000000
## M248_S+lowcyto-M248_C+hicyto 1.0000000
## M248_S+nocyto-M248_C+hicyto 0.0010528
## M248_C+nocyto-M248_C+lowcyto 0.0422944
## M248_S+hicyto-M248_C+lowcyto 1.0000000
## M248_S+lowcyto-M248_C+lowcyto 1.0000000
## M248_S+nocyto-M248_C+lowcyto 0.0011121
## M248_S+hicyto-M248_C+nocyto 0.0743724
## M248_S+lowcyto-M248_C+nocyto 0.0568318
## M248_S+nocyto-M248_C+nocyto 0.9999117
## M248_S+lowcyto-M248_S+hicyto 1.0000000
## M248_S+nocyto-M248_S+hicyto 0.0029721
## M248_S+nocyto-M248_S+lowcyto 0.0018341P7 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P7)
stat.test## LA1511_C+lowcyto LA1511_C+nocyto LA1511_S+hicyto LA1511_S+lowcyto
## "a" "ab" "a" "ab"
## LA1511_S+nocyto M058_C+hicyto M058_C+lowcyto M058_C+nocyto
## "abc" "ab" "a" "ab"
## M058_S+hicyto M058_S+lowcyto M058_S+nocyto M248_C+hicyto
## "ab" "a" "abc" "a"
## M248_C+lowcyto M248_C+nocyto M248_S+hicyto M248_S+lowcyto
## "a" "bc" "ab" "ab"
## M248_S+nocyto LA1511_C+hicyto
## "c" "a"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowcyto"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
Cyto_dataCyto_data$All.condition <- factor(Cyto_data$All.condition, levels = c("C+nocyto", "C+lowcyto", "C+hicyto", "S+nocyto", "S+lowcyto", "S+hicyto"))
Cyto_data2 <- subset(Cyto_data, Cyto_data$Distance.squared < 25)
distance_cyto <- ggplot(data = Cyto_data2, mapping = aes(x = All.condition, y = Distance.squared, colour = All.condition))
distance_cyto <- distance_cyto + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
distance_cyto <- distance_cyto + facet_grid(~ Accession, scales = "free_y")
distance_cyto <- distance_cyto + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
distance_cyto <- distance_cyto + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
distance_cyto <- distance_cyto + ylab("Distance.squared") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 25)
distance_cyto <- distance_cyto + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
distance_cyto <- distance_cyto + rremove("legend")
distance_cyto
####is cyto really fit???? I am not sure...I did not like my plants treated with cyto..it really inhibited their growth by promoting #secondary growth....look at you notes from cyto hormone treatment!!!! for further investigationaov(Alpha ~ All.ID2, data = Cyto_data)## Call:
## aov(formula = Alpha ~ All.ID2, data = Cyto_data)
##
## Terms:
## All.ID2 Residuals
## Sum of Squares 4.256383 7.424220
## Deg. of Freedom 17 144
##
## Residual standard error: 0.2270619
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(Alpha ~ All.ID2, data = Cyto_data))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Alpha ~ All.ID2, data = Cyto_data)
##
## $All.ID2
## diff lwr upr
## LA1511_C+lowcyto-LA1511_C+hicyto -0.057000000 -0.4178176209 0.3038176209
## LA1511_C+nocyto-LA1511_C+hicyto -0.302000000 -0.7186363011 0.1146363011
## LA1511_S+hicyto-LA1511_C+hicyto 0.017000000 -0.3438176209 0.3778176209
## LA1511_S+lowcyto-LA1511_C+hicyto -0.045888889 -0.4165937546 0.3248159769
## LA1511_S+nocyto-LA1511_C+hicyto -0.344000000 -0.7048176209 0.0168176209
## M058_C+hicyto-LA1511_C+hicyto -0.178250000 -0.5609548797 0.2044548797
## M058_C+lowcyto-LA1511_C+hicyto 0.036000000 -0.3248176209 0.3968176209
## M058_C+nocyto-LA1511_C+hicyto 0.045000000 -0.3158176209 0.4058176209
## M058_S+hicyto-LA1511_C+hicyto -0.149500000 -0.5322048797 0.2332048797
## M058_S+lowcyto-LA1511_C+hicyto -0.031000000 -0.3918176209 0.3298176209
## M058_S+nocyto-LA1511_C+hicyto -0.634500000 -1.1118168467 -0.1571831533
## M248_C+hicyto-LA1511_C+hicyto 0.091000000 -0.2698176209 0.4518176209
## M248_C+lowcyto-LA1511_C+hicyto -0.036000000 -0.3968176209 0.3248176209
## M248_C+nocyto-LA1511_C+hicyto -0.112000000 -0.4728176209 0.2488176209
## M248_S+hicyto-LA1511_C+hicyto 0.038000000 -0.3447048797 0.4207048797
## M248_S+lowcyto-LA1511_C+hicyto -0.148111111 -0.5188159769 0.2225937546
## M248_S+nocyto-LA1511_C+hicyto -0.400000000 -0.7608176209 -0.0391823791
## LA1511_C+nocyto-LA1511_C+lowcyto -0.245000000 -0.6616363011 0.1716363011
## LA1511_S+hicyto-LA1511_C+lowcyto 0.074000000 -0.2868176209 0.4348176209
## LA1511_S+lowcyto-LA1511_C+lowcyto 0.011111111 -0.3595937546 0.3818159769
## LA1511_S+nocyto-LA1511_C+lowcyto -0.287000000 -0.6478176209 0.0738176209
## M058_C+hicyto-LA1511_C+lowcyto -0.121250000 -0.5039548797 0.2614548797
## M058_C+lowcyto-LA1511_C+lowcyto 0.093000000 -0.2678176209 0.4538176209
## M058_C+nocyto-LA1511_C+lowcyto 0.102000000 -0.2588176209 0.4628176209
## M058_S+hicyto-LA1511_C+lowcyto -0.092500000 -0.4752048797 0.2902048797
## M058_S+lowcyto-LA1511_C+lowcyto 0.026000000 -0.3348176209 0.3868176209
## M058_S+nocyto-LA1511_C+lowcyto -0.577500000 -1.0548168467 -0.1001831533
## M248_C+hicyto-LA1511_C+lowcyto 0.148000000 -0.2128176209 0.5088176209
## M248_C+lowcyto-LA1511_C+lowcyto 0.021000000 -0.3398176209 0.3818176209
## M248_C+nocyto-LA1511_C+lowcyto -0.055000000 -0.4158176209 0.3058176209
## M248_S+hicyto-LA1511_C+lowcyto 0.095000000 -0.2877048797 0.4777048797
## M248_S+lowcyto-LA1511_C+lowcyto -0.091111111 -0.4618159769 0.2795937546
## M248_S+nocyto-LA1511_C+lowcyto -0.343000000 -0.7038176209 0.0178176209
## LA1511_S+hicyto-LA1511_C+nocyto 0.319000000 -0.0976363011 0.7356363011
## LA1511_S+lowcyto-LA1511_C+nocyto 0.256111111 -0.1691165330 0.6813387552
## LA1511_S+nocyto-LA1511_C+nocyto -0.042000000 -0.4586363011 0.3746363011
## M058_C+hicyto-LA1511_C+nocyto 0.123750000 -0.3119786734 0.5594786734
## M058_C+lowcyto-LA1511_C+nocyto 0.338000000 -0.0786363011 0.7546363011
## M058_C+nocyto-LA1511_C+nocyto 0.347000000 -0.0696363011 0.7636363011
## M058_S+hicyto-LA1511_C+nocyto 0.152500000 -0.2832286734 0.5882286734
## M058_S+lowcyto-LA1511_C+nocyto 0.271000000 -0.1456363011 0.6876363011
## M058_S+nocyto-LA1511_C+nocyto -0.332500000 -0.8532953763 0.1882953763
## M248_C+hicyto-LA1511_C+nocyto 0.393000000 -0.0236363011 0.8096363011
## M248_C+lowcyto-LA1511_C+nocyto 0.266000000 -0.1506363011 0.6826363011
## M248_C+nocyto-LA1511_C+nocyto 0.190000000 -0.2266363011 0.6066363011
## M248_S+hicyto-LA1511_C+nocyto 0.340000000 -0.0957286734 0.7757286734
## M248_S+lowcyto-LA1511_C+nocyto 0.153888889 -0.2713387552 0.5791165330
## M248_S+nocyto-LA1511_C+nocyto -0.098000000 -0.5146363011 0.3186363011
## LA1511_S+lowcyto-LA1511_S+hicyto -0.062888889 -0.4335937546 0.3078159769
## LA1511_S+nocyto-LA1511_S+hicyto -0.361000000 -0.7218176209 -0.0001823791
## M058_C+hicyto-LA1511_S+hicyto -0.195250000 -0.5779548797 0.1874548797
## M058_C+lowcyto-LA1511_S+hicyto 0.019000000 -0.3418176209 0.3798176209
## M058_C+nocyto-LA1511_S+hicyto 0.028000000 -0.3328176209 0.3888176209
## M058_S+hicyto-LA1511_S+hicyto -0.166500000 -0.5492048797 0.2162048797
## M058_S+lowcyto-LA1511_S+hicyto -0.048000000 -0.4088176209 0.3128176209
## M058_S+nocyto-LA1511_S+hicyto -0.651500000 -1.1288168467 -0.1741831533
## M248_C+hicyto-LA1511_S+hicyto 0.074000000 -0.2868176209 0.4348176209
## M248_C+lowcyto-LA1511_S+hicyto -0.053000000 -0.4138176209 0.3078176209
## M248_C+nocyto-LA1511_S+hicyto -0.129000000 -0.4898176209 0.2318176209
## M248_S+hicyto-LA1511_S+hicyto 0.021000000 -0.3617048797 0.4037048797
## M248_S+lowcyto-LA1511_S+hicyto -0.165111111 -0.5358159769 0.2055937546
## M248_S+nocyto-LA1511_S+hicyto -0.417000000 -0.7778176209 -0.0561823791
## LA1511_S+nocyto-LA1511_S+lowcyto -0.298111111 -0.6688159769 0.0725937546
## M058_C+hicyto-LA1511_S+lowcyto -0.132361111 -0.5244016281 0.2596794058
## M058_C+lowcyto-LA1511_S+lowcyto 0.081888889 -0.2888159769 0.4525937546
## M058_C+nocyto-LA1511_S+lowcyto 0.090888889 -0.2798159769 0.4615937546
## M058_S+hicyto-LA1511_S+lowcyto -0.103611111 -0.4956516281 0.2884294058
## M058_S+lowcyto-LA1511_S+lowcyto 0.014888889 -0.3558159769 0.3855937546
## M058_S+nocyto-LA1511_S+lowcyto -0.588611111 -1.0734452210 -0.1037770012
## M248_C+hicyto-LA1511_S+lowcyto 0.136888889 -0.2338159769 0.5075937546
## M248_C+lowcyto-LA1511_S+lowcyto 0.009888889 -0.3608159769 0.3805937546
## M248_C+nocyto-LA1511_S+lowcyto -0.066111111 -0.4368159769 0.3045937546
## M248_S+hicyto-LA1511_S+lowcyto 0.083888889 -0.3081516281 0.4759294058
## M248_S+lowcyto-LA1511_S+lowcyto -0.102222222 -0.4825573895 0.2781129451
## M248_S+nocyto-LA1511_S+lowcyto -0.354111111 -0.7248159769 0.0165937546
## M058_C+hicyto-LA1511_S+nocyto 0.165750000 -0.2169548797 0.5484548797
## M058_C+lowcyto-LA1511_S+nocyto 0.380000000 0.0191823791 0.7408176209
## M058_C+nocyto-LA1511_S+nocyto 0.389000000 0.0281823791 0.7498176209
## M058_S+hicyto-LA1511_S+nocyto 0.194500000 -0.1882048797 0.5772048797
## M058_S+lowcyto-LA1511_S+nocyto 0.313000000 -0.0478176209 0.6738176209
## M058_S+nocyto-LA1511_S+nocyto -0.290500000 -0.7678168467 0.1868168467
## M248_C+hicyto-LA1511_S+nocyto 0.435000000 0.0741823791 0.7958176209
## M248_C+lowcyto-LA1511_S+nocyto 0.308000000 -0.0528176209 0.6688176209
## M248_C+nocyto-LA1511_S+nocyto 0.232000000 -0.1288176209 0.5928176209
## M248_S+hicyto-LA1511_S+nocyto 0.382000000 -0.0007048797 0.7647048797
## M248_S+lowcyto-LA1511_S+nocyto 0.195888889 -0.1748159769 0.5665937546
## M248_S+nocyto-LA1511_S+nocyto -0.056000000 -0.4168176209 0.3048176209
## M058_C+lowcyto-M058_C+hicyto 0.214250000 -0.1684548797 0.5969548797
## M058_C+nocyto-M058_C+hicyto 0.223250000 -0.1594548797 0.6059548797
## M058_S+hicyto-M058_C+hicyto 0.028750000 -0.3746563639 0.4321563639
## M058_S+lowcyto-M058_C+hicyto 0.147250000 -0.2354548797 0.5299548797
## M058_S+nocyto-M058_C+hicyto -0.456250000 -0.9503198752 0.0378198752
## M248_C+hicyto-M058_C+hicyto 0.269250000 -0.1134548797 0.6519548797
## M248_C+lowcyto-M058_C+hicyto 0.142250000 -0.2404548797 0.5249548797
## M248_C+nocyto-M058_C+hicyto 0.066250000 -0.3164548797 0.4489548797
## M248_S+hicyto-M058_C+hicyto 0.216250000 -0.1871563639 0.6196563639
## M248_S+lowcyto-M058_C+hicyto 0.030138889 -0.3619016281 0.4221794058
## M248_S+nocyto-M058_C+hicyto -0.221750000 -0.6044548797 0.1609548797
## M058_C+nocyto-M058_C+lowcyto 0.009000000 -0.3518176209 0.3698176209
## M058_S+hicyto-M058_C+lowcyto -0.185500000 -0.5682048797 0.1972048797
## M058_S+lowcyto-M058_C+lowcyto -0.067000000 -0.4278176209 0.2938176209
## M058_S+nocyto-M058_C+lowcyto -0.670500000 -1.1478168467 -0.1931831533
## M248_C+hicyto-M058_C+lowcyto 0.055000000 -0.3058176209 0.4158176209
## M248_C+lowcyto-M058_C+lowcyto -0.072000000 -0.4328176209 0.2888176209
## M248_C+nocyto-M058_C+lowcyto -0.148000000 -0.5088176209 0.2128176209
## M248_S+hicyto-M058_C+lowcyto 0.002000000 -0.3807048797 0.3847048797
## M248_S+lowcyto-M058_C+lowcyto -0.184111111 -0.5548159769 0.1865937546
## M248_S+nocyto-M058_C+lowcyto -0.436000000 -0.7968176209 -0.0751823791
## M058_S+hicyto-M058_C+nocyto -0.194500000 -0.5772048797 0.1882048797
## M058_S+lowcyto-M058_C+nocyto -0.076000000 -0.4368176209 0.2848176209
## M058_S+nocyto-M058_C+nocyto -0.679500000 -1.1568168467 -0.2021831533
## M248_C+hicyto-M058_C+nocyto 0.046000000 -0.3148176209 0.4068176209
## M248_C+lowcyto-M058_C+nocyto -0.081000000 -0.4418176209 0.2798176209
## M248_C+nocyto-M058_C+nocyto -0.157000000 -0.5178176209 0.2038176209
## M248_S+hicyto-M058_C+nocyto -0.007000000 -0.3897048797 0.3757048797
## M248_S+lowcyto-M058_C+nocyto -0.193111111 -0.5638159769 0.1775937546
## M248_S+nocyto-M058_C+nocyto -0.445000000 -0.8058176209 -0.0841823791
## M058_S+lowcyto-M058_S+hicyto 0.118500000 -0.2642048797 0.5012048797
## M058_S+nocyto-M058_S+hicyto -0.485000000 -0.9790698752 0.0090698752
## M248_C+hicyto-M058_S+hicyto 0.240500000 -0.1422048797 0.6232048797
## M248_C+lowcyto-M058_S+hicyto 0.113500000 -0.2692048797 0.4962048797
## M248_C+nocyto-M058_S+hicyto 0.037500000 -0.3452048797 0.4202048797
## M248_S+hicyto-M058_S+hicyto 0.187500000 -0.2159063639 0.5909063639
## M248_S+lowcyto-M058_S+hicyto 0.001388889 -0.3906516281 0.3934294058
## M248_S+nocyto-M058_S+hicyto -0.250500000 -0.6332048797 0.1322048797
## M058_S+nocyto-M058_S+lowcyto -0.603500000 -1.0808168467 -0.1261831533
## M248_C+hicyto-M058_S+lowcyto 0.122000000 -0.2388176209 0.4828176209
## M248_C+lowcyto-M058_S+lowcyto -0.005000000 -0.3658176209 0.3558176209
## M248_C+nocyto-M058_S+lowcyto -0.081000000 -0.4418176209 0.2798176209
## M248_S+hicyto-M058_S+lowcyto 0.069000000 -0.3137048797 0.4517048797
## M248_S+lowcyto-M058_S+lowcyto -0.117111111 -0.4878159769 0.2535937546
## M248_S+nocyto-M058_S+lowcyto -0.369000000 -0.7298176209 -0.0081823791
## M248_C+hicyto-M058_S+nocyto 0.725500000 0.2481831533 1.2028168467
## M248_C+lowcyto-M058_S+nocyto 0.598500000 0.1211831533 1.0758168467
## M248_C+nocyto-M058_S+nocyto 0.522500000 0.0451831533 0.9998168467
## M248_S+hicyto-M058_S+nocyto 0.672500000 0.1784301248 1.1665698752
## M248_S+lowcyto-M058_S+nocyto 0.486388889 0.0015547790 0.9712229988
## M248_S+nocyto-M058_S+nocyto 0.234500000 -0.2428168467 0.7118168467
## M248_C+lowcyto-M248_C+hicyto -0.127000000 -0.4878176209 0.2338176209
## M248_C+nocyto-M248_C+hicyto -0.203000000 -0.5638176209 0.1578176209
## M248_S+hicyto-M248_C+hicyto -0.053000000 -0.4357048797 0.3297048797
## M248_S+lowcyto-M248_C+hicyto -0.239111111 -0.6098159769 0.1315937546
## M248_S+nocyto-M248_C+hicyto -0.491000000 -0.8518176209 -0.1301823791
## M248_C+nocyto-M248_C+lowcyto -0.076000000 -0.4368176209 0.2848176209
## M248_S+hicyto-M248_C+lowcyto 0.074000000 -0.3087048797 0.4567048797
## M248_S+lowcyto-M248_C+lowcyto -0.112111111 -0.4828159769 0.2585937546
## M248_S+nocyto-M248_C+lowcyto -0.364000000 -0.7248176209 -0.0031823791
## M248_S+hicyto-M248_C+nocyto 0.150000000 -0.2327048797 0.5327048797
## M248_S+lowcyto-M248_C+nocyto -0.036111111 -0.4068159769 0.3345937546
## M248_S+nocyto-M248_C+nocyto -0.288000000 -0.6488176209 0.0728176209
## M248_S+lowcyto-M248_S+hicyto -0.186111111 -0.5781516281 0.2059294058
## M248_S+nocyto-M248_S+hicyto -0.438000000 -0.8207048797 -0.0552951203
## M248_S+nocyto-M248_S+lowcyto -0.251888889 -0.6225937546 0.1188159769
## p adj
## LA1511_C+lowcyto-LA1511_C+hicyto 1.0000000
## LA1511_C+nocyto-LA1511_C+hicyto 0.4784179
## LA1511_S+hicyto-LA1511_C+hicyto 1.0000000
## LA1511_S+lowcyto-LA1511_C+hicyto 1.0000000
## LA1511_S+nocyto-LA1511_C+hicyto 0.0807471
## M058_C+hicyto-LA1511_C+hicyto 0.9716720
## M058_C+lowcyto-LA1511_C+hicyto 1.0000000
## M058_C+nocyto-LA1511_C+hicyto 1.0000000
## M058_S+hicyto-LA1511_C+hicyto 0.9954515
## M058_S+lowcyto-LA1511_C+hicyto 1.0000000
## M058_S+nocyto-LA1511_C+hicyto 0.0007398
## M248_C+hicyto-LA1511_C+hicyto 0.9999846
## M248_C+lowcyto-LA1511_C+hicyto 1.0000000
## M248_C+nocyto-LA1511_C+hicyto 0.9997300
## M248_S+hicyto-LA1511_C+hicyto 1.0000000
## M248_S+lowcyto-LA1511_C+hicyto 0.9941476
## M248_S+nocyto-LA1511_C+hicyto 0.0144436
## LA1511_C+nocyto-LA1511_C+lowcyto 0.8176725
## LA1511_S+hicyto-LA1511_C+lowcyto 0.9999993
## LA1511_S+lowcyto-LA1511_C+lowcyto 1.0000000
## LA1511_S+nocyto-LA1511_C+lowcyto 0.3087856
## M058_C+hicyto-LA1511_C+lowcyto 0.9996470
## M058_C+lowcyto-LA1511_C+lowcyto 0.9999790
## M058_C+nocyto-LA1511_C+lowcyto 0.9999234
## M058_S+hicyto-LA1511_C+lowcyto 0.9999917
## M058_S+lowcyto-LA1511_C+lowcyto 1.0000000
## M058_S+nocyto-LA1511_C+lowcyto 0.0039494
## M248_C+hicyto-LA1511_C+lowcyto 0.9921957
## M248_C+lowcyto-LA1511_C+lowcyto 1.0000000
## M248_C+nocyto-LA1511_C+lowcyto 1.0000000
## M248_S+hicyto-LA1511_C+lowcyto 0.9999878
## M248_S+lowcyto-LA1511_C+lowcyto 0.9999894
## M248_S+nocyto-LA1511_C+lowcyto 0.0829899
## LA1511_S+hicyto-LA1511_C+nocyto 0.3763040
## LA1511_S+lowcyto-LA1511_C+nocyto 0.7880184
## LA1511_S+nocyto-LA1511_C+nocyto 1.0000000
## M058_C+hicyto-LA1511_C+nocyto 0.9999184
## M058_C+lowcyto-LA1511_C+nocyto 0.2758367
## M058_C+nocyto-LA1511_C+nocyto 0.2345631
## M058_S+hicyto-LA1511_C+nocyto 0.9987556
## M058_S+lowcyto-LA1511_C+nocyto 0.6738703
## M058_S+nocyto-LA1511_C+nocyto 0.7039656
## M248_C+hicyto-LA1511_C+nocyto 0.0891890
## M248_C+lowcyto-LA1511_C+nocyto 0.7039656
## M248_C+nocyto-LA1511_C+nocyto 0.9768489
## M248_S+hicyto-LA1511_C+nocyto 0.3422080
## M248_S+lowcyto-LA1511_C+nocyto 0.9981327
## M248_S+nocyto-LA1511_C+nocyto 0.9999944
## LA1511_S+lowcyto-LA1511_S+hicyto 1.0000000
## LA1511_S+nocyto-LA1511_S+hicyto 0.0497315
## M058_C+hicyto-LA1511_S+hicyto 0.9363234
## M058_C+lowcyto-LA1511_S+hicyto 1.0000000
## M058_C+nocyto-LA1511_S+hicyto 1.0000000
## M058_S+hicyto-LA1511_S+hicyto 0.9855036
## M058_S+lowcyto-LA1511_S+hicyto 1.0000000
## M058_S+nocyto-LA1511_S+hicyto 0.0004369
## M248_C+hicyto-LA1511_S+hicyto 0.9999993
## M248_C+lowcyto-LA1511_S+hicyto 1.0000000
## M248_C+nocyto-LA1511_S+hicyto 0.9983871
## M248_S+hicyto-LA1511_S+hicyto 1.0000000
## M248_S+lowcyto-LA1511_S+hicyto 0.9816346
## M248_S+nocyto-LA1511_S+hicyto 0.0080242
## LA1511_S+nocyto-LA1511_S+lowcyto 0.2902990
## M058_C+hicyto-LA1511_S+lowcyto 0.9992038
## M058_C+lowcyto-LA1511_S+lowcyto 0.9999978
## M058_C+nocyto-LA1511_S+lowcyto 0.9999898
## M058_S+hicyto-LA1511_S+lowcyto 0.9999701
## M058_S+lowcyto-LA1511_S+lowcyto 1.0000000
## M058_S+nocyto-LA1511_S+lowcyto 0.0037351
## M248_C+hicyto-LA1511_S+lowcyto 0.9976264
## M248_C+lowcyto-LA1511_S+lowcyto 1.0000000
## M248_C+nocyto-LA1511_S+lowcyto 0.9999999
## M248_S+hicyto-LA1511_S+lowcyto 0.9999986
## M248_S+lowcyto-LA1511_S+lowcyto 0.9999621
## M248_S+nocyto-LA1511_S+lowcyto 0.0792806
## M058_C+hicyto-LA1511_S+nocyto 0.9861578
## M058_C+lowcyto-LA1511_S+nocyto 0.0277943
## M058_C+nocyto-LA1511_S+nocyto 0.0208094
## M058_S+hicyto-LA1511_S+nocyto 0.9383385
## M058_S+lowcyto-LA1511_S+nocyto 0.1774741
## M058_S+nocyto-LA1511_S+nocyto 0.7741825
## M248_C+hicyto-LA1511_S+nocyto 0.0041827
## M248_C+lowcyto-LA1511_S+nocyto 0.1989911
## M248_C+nocyto-LA1511_S+nocyto 0.6926895
## M248_S+hicyto-LA1511_S+nocyto 0.0509890
## M248_S+lowcyto-LA1511_S+nocyto 0.9153430
## M248_S+nocyto-LA1511_S+nocyto 1.0000000
## M058_C+lowcyto-M058_C+hicyto 0.8694295
## M058_C+nocyto-M058_C+hicyto 0.8269470
## M058_S+hicyto-M058_C+hicyto 1.0000000
## M058_S+lowcyto-M058_C+hicyto 0.9961718
## M058_S+nocyto-M058_C+hicyto 0.1078172
## M248_C+hicyto-M058_C+hicyto 0.5344537
## M248_C+lowcyto-M058_C+hicyto 0.9974357
## M248_C+nocyto-M058_C+hicyto 0.9999999
## M248_S+hicyto-M058_C+hicyto 0.9053314
## M248_S+lowcyto-M058_C+hicyto 1.0000000
## M248_S+nocyto-M058_C+hicyto 0.8344925
## M058_C+nocyto-M058_C+lowcyto 1.0000000
## M058_S+hicyto-M058_C+lowcyto 0.9591170
## M058_S+lowcyto-M058_C+lowcyto 0.9999998
## M058_S+nocyto-M058_C+lowcyto 0.0002392
## M248_C+hicyto-M058_C+lowcyto 1.0000000
## M248_C+lowcyto-M058_C+lowcyto 0.9999995
## M248_C+nocyto-M058_C+lowcyto 0.9921957
## M248_S+hicyto-M058_C+lowcyto 1.0000000
## M248_S+lowcyto-M058_C+lowcyto 0.9493309
## M248_S+nocyto-M058_C+lowcyto 0.0040306
## M058_S+hicyto-M058_C+nocyto 0.9383385
## M058_S+lowcyto-M058_C+nocyto 0.9999989
## M058_S+nocyto-M058_C+nocyto 0.0001790
## M248_C+hicyto-M058_C+nocyto 1.0000000
## M248_C+lowcyto-M058_C+nocyto 0.9999972
## M248_C+nocyto-M058_C+nocyto 0.9854826
## M248_S+hicyto-M058_C+nocyto 1.0000000
## M248_S+lowcyto-M058_C+nocyto 0.9244561
## M248_S+nocyto-M058_C+nocyto 0.0028772
## M058_S+lowcyto-M058_S+hicyto 0.9997387
## M058_S+nocyto-M058_S+hicyto 0.0606372
## M248_C+hicyto-M058_S+hicyto 0.7283714
## M248_C+lowcyto-M058_S+hicyto 0.9998529
## M248_C+nocyto-M058_S+hicyto 1.0000000
## M248_S+hicyto-M058_S+hicyto 0.9722255
## M248_S+lowcyto-M058_S+hicyto 1.0000000
## M248_S+nocyto-M058_S+hicyto 0.6633924
## M058_S+nocyto-M058_S+lowcyto 0.0018735
## M248_C+hicyto-M058_S+lowcyto 0.9991889
## M248_C+lowcyto-M058_S+lowcyto 1.0000000
## M248_C+nocyto-M058_S+lowcyto 0.9999972
## M248_S+hicyto-M058_S+lowcyto 0.9999999
## M248_S+lowcyto-M058_S+lowcyto 0.9996600
## M248_S+nocyto-M058_S+lowcyto 0.0391201
## M248_C+hicyto-M058_S+nocyto 0.0000388
## M248_C+lowcyto-M058_S+nocyto 0.0021677
## M248_C+nocyto-M058_S+nocyto 0.0170927
## M248_S+hicyto-M058_S+nocyto 0.0004622
## M248_S+lowcyto-M058_S+nocyto 0.0483175
## M248_S+nocyto-M058_S+nocyto 0.9539151
## M248_C+lowcyto-M248_C+hicyto 0.9986662
## M248_C+nocyto-M248_C+hicyto 0.8647624
## M248_S+hicyto-M248_C+hicyto 1.0000000
## M248_S+lowcyto-M248_C+hicyto 0.6875945
## M248_S+nocyto-M248_C+hicyto 0.0004646
## M248_C+nocyto-M248_C+lowcyto 0.9999989
## M248_S+hicyto-M248_C+lowcyto 0.9999997
## M248_S+lowcyto-M248_C+lowcyto 0.9998088
## M248_S+nocyto-M248_C+lowcyto 0.0454906
## M248_S+hicyto-M248_C+nocyto 0.9952769
## M248_S+lowcyto-M248_C+nocyto 1.0000000
## M248_S+nocyto-M248_C+nocyto 0.3028637
## M248_S+lowcyto-M248_S+hicyto 0.9661630
## M248_S+nocyto-M248_S+hicyto 0.0092533
## M248_S+nocyto-M248_S+lowcyto 0.5982985P8 = Output$All.ID2[,'p adj']
stat.test<- multcompLetters(P8)
stat.test## LA1511_C+lowcyto LA1511_C+nocyto LA1511_S+hicyto LA1511_S+lowcyto
## "abc" "abcd" "a" "abc"
## LA1511_S+nocyto M058_C+hicyto M058_C+lowcyto M058_C+nocyto
## "bcd" "abcd" "a" "a"
## M058_S+hicyto M058_S+lowcyto M058_S+nocyto M248_C+hicyto
## "abcd" "ab" "d" "a"
## M248_C+lowcyto M248_C+nocyto M248_S+hicyto M248_S+lowcyto
## "ab" "abc" "ab" "abc"
## M248_S+nocyto LA1511_C+hicyto
## "cd" "ab"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testtest$info <- strsplit(test$group1, "_")
test$info[[1]][2]## [1] "C+lowcyto"test$Accession <- "none"
test$All.condition<- "none"
testfor(i in 1:nrow(test)){
test$Accession[i] <- test$info[[i]][1]
test$All.condition[i] <- test$info[[i]][2]
}
test2 <- test[,c(5:6,1)]
test2$group1 <- test2$All.condition
test2$group2 <- test2$All.condition
Cyto_dataCyto_data$All.condition <- factor(Cyto_data$All.condition, levels = c("C+nocyto", "C+lowcyto", "C+hicyto", "S+nocyto", "S+lowcyto", "S+hicyto"))
#Cyto_data2 <- subset(Cyto_data, Cyto_data$Distance.squared < 25)
Alpha_cyto <- ggplot(data = Cyto_data, mapping = aes(x = All.condition, y = Alpha, colour = All.condition))
Alpha_cyto <- Alpha_cyto + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Alpha_cyto <- Alpha_cyto + facet_grid(~ Accession, scales = "free_y")
Alpha_cyto <- Alpha_cyto + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Alpha_cyto <- Alpha_cyto + scale_color_manual(values = c("blueviolet","cyan", "pink", "red1","green","magenta"))
Alpha_cyto <- Alpha_cyto + ylab("Alpha") + xlab("")+stat_pvalue_manual(test2, label = "Tukey", y.position = 1.2)
Alpha_cyto <- Alpha_cyto + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Alpha_cyto <- Alpha_cyto + rremove("legend")
Alpha_cyto
Maryam conclusion:
ACC: Based on ICP analysis, ACC treatment appears suitable for alleviating salt stress across all three accessions. The previous Pareto analysis indicated that ACC was effective for two accessions but not for LA, which was a concern. However, the new analysis suggests ACC is also effective for LA at low concentrations. Additionally, the updated Pareto analysis shows that ACC treatment uniformly drives all root topologies towards a TP structure.
IAA: My ICCP analysis indicates that IAA treatment is not beneficial for any of the three accessions. The new Pareto analysis suggested IAA is effective for accession 248 but not for the others, which does not align with our observations. Moreover, the updated alpha analysis shows that LA and 058 exhibit less TP root topology compared to 248. However, our direct observations clearly showed that all root types display a TP structure when treated with IAA under salt conditions.