This is a pareto-front components calculation for 3 tomatoes experienced ABA and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220606_RSA_M248M058LA1511_ABA_100mM_Salt_2days. The root tracing was done by REU student YALMARIE NUMAN-VAZQUEZ in summer 2022.
getwd()
## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20220729_ABA_pareto-front_components_1st_experiment"
list.files(pattern = ".csv")
## [1] "scaling_distances_modified_ABA.csv"
ABA_pareto_location <-read.csv("scaling_distances_modified_ABA.csv")
ABA_pareto_location
ABA_pareto_location$Condition.all <- paste(ABA_pareto_location$Condition, ABA_pareto_location$Condition2, sep="_")
ABA_pareto_location
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 4.0.5
library(ggpubr)
## Warning: package 'ggpubr' was built under R version 4.0.5
library(multcompView)
## Warning: package 'multcompView' was built under R version 4.0.5
ABA_pareto_location$All.ID <- paste(ABA_pareto_location$Accessions, ABA_pareto_location$Condition.all, ABA_pareto_location$Day, sep="_")
ABA_pareto_location
aov(pareto.front.scaling.location ~ All.ID, data = ABA_pareto_location)
## Call:
## aov(formula = pareto.front.scaling.location ~ All.ID, data = ABA_pareto_location)
##
## Terms:
## All.ID Residuals
## Sum of Squares 6.082270 4.626644
## Deg. of Freedom 17 145
##
## Residual standard error: 0.1786278
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.scaling.location ~ All.ID, data = ABA_pareto_location))
Output
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = pareto.front.scaling.location ~ All.ID, data = ABA_pareto_location)
##
## $All.ID
## diff lwr upr
## LA1511_C_1aba_9-LA1511_C_10aba_9 0.0180000000 -0.283033058 0.319033058
## LA1511_C_noaba_9-LA1511_C_10aba_9 0.0857777778 -0.205816150 0.377371706
## LA1511_S_10aba_9-LA1511_C_10aba_9 0.1313333333 -0.196389950 0.459056616
## LA1511_S_1aba_9-LA1511_C_10aba_9 0.0640000000 -0.219816689 0.347816689
## LA1511_S_noaba_9-LA1511_C_10aba_9 0.1660000000 -0.117816689 0.449816689
## M058_C_10aba_9-LA1511_C_10aba_9 0.6390000000 0.355183311 0.922816689
## M058_C_1aba_9-LA1511_C_10aba_9 0.0780000000 -0.234750758 0.390750758
## M058_C_noaba_9-LA1511_C_10aba_9 0.2100000000 -0.073816689 0.493816689
## M058_S_10aba_9-LA1511_C_10aba_9 0.3555000000 0.054466942 0.656533058
## M058_S_1aba_9-LA1511_C_10aba_9 0.5210000000 0.237183311 0.804816689
## M058_S_noaba_9-LA1511_C_10aba_9 0.2090000000 -0.074816689 0.492816689
## M248_C_10aba_9-LA1511_C_10aba_9 -0.0550000000 -0.338816689 0.228816689
## M248_C_1aba_9-LA1511_C_10aba_9 0.0008571429 -0.311893616 0.313607901
## M248_C_noaba_9-LA1511_C_10aba_9 0.3160000000 0.032183311 0.599816689
## M248_S_10aba_9-LA1511_C_10aba_9 0.0224444444 -0.269149484 0.314038373
## M248_S_1aba_9-LA1511_C_10aba_9 -0.0240000000 -0.307816689 0.259816689
## M248_S_noaba_9-LA1511_C_10aba_9 0.0413333333 -0.250260595 0.332927262
## LA1511_C_noaba_9-LA1511_C_1aba_9 0.0677777778 -0.240598629 0.376154184
## LA1511_S_10aba_9-LA1511_C_1aba_9 0.1133333333 -0.229407880 0.456074547
## LA1511_S_1aba_9-LA1511_C_1aba_9 0.0460000000 -0.255033058 0.347033058
## LA1511_S_noaba_9-LA1511_C_1aba_9 0.1480000000 -0.153033058 0.449033058
## M058_C_10aba_9-LA1511_C_1aba_9 0.6210000000 0.319966942 0.922033058
## M058_C_1aba_9-LA1511_C_1aba_9 0.0600000000 -0.268453994 0.388453994
## M058_C_noaba_9-LA1511_C_1aba_9 0.1920000000 -0.109033058 0.493033058
## M058_S_10aba_9-LA1511_C_1aba_9 0.3375000000 0.020183296 0.654816704
## M058_S_1aba_9-LA1511_C_1aba_9 0.5030000000 0.201966942 0.804033058
## M058_S_noaba_9-LA1511_C_1aba_9 0.1910000000 -0.110033058 0.492033058
## M248_C_10aba_9-LA1511_C_1aba_9 -0.0730000000 -0.374033058 0.228033058
## M248_C_1aba_9-LA1511_C_1aba_9 -0.0171428571 -0.345596851 0.311311137
## M248_C_noaba_9-LA1511_C_1aba_9 0.2980000000 -0.003033058 0.599033058
## M248_S_10aba_9-LA1511_C_1aba_9 0.0044444444 -0.303931962 0.312820851
## M248_S_1aba_9-LA1511_C_1aba_9 -0.0420000000 -0.343033058 0.259033058
## M248_S_noaba_9-LA1511_C_1aba_9 0.0233333333 -0.285043073 0.331709740
## LA1511_S_10aba_9-LA1511_C_noaba_9 0.0455555556 -0.288925620 0.380036731
## LA1511_S_1aba_9-LA1511_C_noaba_9 -0.0217777778 -0.313371706 0.269816150
## LA1511_S_noaba_9-LA1511_C_noaba_9 0.0802222222 -0.211371706 0.371816150
## M058_C_10aba_9-LA1511_C_noaba_9 0.5532222222 0.261628294 0.844816150
## M058_C_1aba_9-LA1511_C_noaba_9 -0.0077777778 -0.327602954 0.312047398
## M058_C_noaba_9-LA1511_C_noaba_9 0.1242222222 -0.167371706 0.415816150
## M058_S_10aba_9-LA1511_C_noaba_9 0.2697222222 -0.038654184 0.578098629
## M058_S_1aba_9-LA1511_C_noaba_9 0.4352222222 0.143628294 0.726816150
## M058_S_noaba_9-LA1511_C_noaba_9 0.1232222222 -0.168371706 0.414816150
## M248_C_10aba_9-LA1511_C_noaba_9 -0.1407777778 -0.432371706 0.150816150
## M248_C_1aba_9-LA1511_C_noaba_9 -0.0849206349 -0.404745811 0.234904541
## M248_C_noaba_9-LA1511_C_noaba_9 0.2302222222 -0.061371706 0.521816150
## M248_S_10aba_9-LA1511_C_noaba_9 -0.0633333333 -0.362502391 0.235835725
## M248_S_1aba_9-LA1511_C_noaba_9 -0.1097777778 -0.401371706 0.181816150
## M248_S_noaba_9-LA1511_C_noaba_9 -0.0444444444 -0.343613502 0.254724614
## LA1511_S_1aba_9-LA1511_S_10aba_9 -0.0673333333 -0.395056616 0.260389950
## LA1511_S_noaba_9-LA1511_S_10aba_9 0.0346666667 -0.293056616 0.362389950
## M058_C_10aba_9-LA1511_S_10aba_9 0.5076666667 0.179943384 0.835389950
## M058_C_1aba_9-LA1511_S_10aba_9 -0.0533333333 -0.406410767 0.299744101
## M058_C_noaba_9-LA1511_S_10aba_9 0.0786666667 -0.249056616 0.406389950
## M058_S_10aba_9-LA1511_S_10aba_9 0.2241666667 -0.118574547 0.566907880
## M058_S_1aba_9-LA1511_S_10aba_9 0.3896666667 0.061943384 0.717389950
## M058_S_noaba_9-LA1511_S_10aba_9 0.0776666667 -0.250056616 0.405389950
## M248_C_10aba_9-LA1511_S_10aba_9 -0.1863333333 -0.514056616 0.141389950
## M248_C_1aba_9-LA1511_S_10aba_9 -0.1304761905 -0.483553625 0.222601244
## M248_C_noaba_9-LA1511_S_10aba_9 0.1846666667 -0.143056616 0.512389950
## M248_S_10aba_9-LA1511_S_10aba_9 -0.1088888889 -0.443370064 0.225592286
## M248_S_1aba_9-LA1511_S_10aba_9 -0.1553333333 -0.483056616 0.172389950
## M248_S_noaba_9-LA1511_S_10aba_9 -0.0900000000 -0.424481175 0.244481175
## LA1511_S_noaba_9-LA1511_S_1aba_9 0.1020000000 -0.181816689 0.385816689
## M058_C_10aba_9-LA1511_S_1aba_9 0.5750000000 0.291183311 0.858816689
## M058_C_1aba_9-LA1511_S_1aba_9 0.0140000000 -0.298750758 0.326750758
## M058_C_noaba_9-LA1511_S_1aba_9 0.1460000000 -0.137816689 0.429816689
## M058_S_10aba_9-LA1511_S_1aba_9 0.2915000000 -0.009533058 0.592533058
## M058_S_1aba_9-LA1511_S_1aba_9 0.4570000000 0.173183311 0.740816689
## M058_S_noaba_9-LA1511_S_1aba_9 0.1450000000 -0.138816689 0.428816689
## M248_C_10aba_9-LA1511_S_1aba_9 -0.1190000000 -0.402816689 0.164816689
## M248_C_1aba_9-LA1511_S_1aba_9 -0.0631428571 -0.375893616 0.249607901
## M248_C_noaba_9-LA1511_S_1aba_9 0.2520000000 -0.031816689 0.535816689
## M248_S_10aba_9-LA1511_S_1aba_9 -0.0415555556 -0.333149484 0.250038373
## M248_S_1aba_9-LA1511_S_1aba_9 -0.0880000000 -0.371816689 0.195816689
## M248_S_noaba_9-LA1511_S_1aba_9 -0.0226666667 -0.314260595 0.268927262
## M058_C_10aba_9-LA1511_S_noaba_9 0.4730000000 0.189183311 0.756816689
## M058_C_1aba_9-LA1511_S_noaba_9 -0.0880000000 -0.400750758 0.224750758
## M058_C_noaba_9-LA1511_S_noaba_9 0.0440000000 -0.239816689 0.327816689
## M058_S_10aba_9-LA1511_S_noaba_9 0.1895000000 -0.111533058 0.490533058
## M058_S_1aba_9-LA1511_S_noaba_9 0.3550000000 0.071183311 0.638816689
## M058_S_noaba_9-LA1511_S_noaba_9 0.0430000000 -0.240816689 0.326816689
## M248_C_10aba_9-LA1511_S_noaba_9 -0.2210000000 -0.504816689 0.062816689
## M248_C_1aba_9-LA1511_S_noaba_9 -0.1651428571 -0.477893616 0.147607901
## M248_C_noaba_9-LA1511_S_noaba_9 0.1500000000 -0.133816689 0.433816689
## M248_S_10aba_9-LA1511_S_noaba_9 -0.1435555556 -0.435149484 0.148038373
## M248_S_1aba_9-LA1511_S_noaba_9 -0.1900000000 -0.473816689 0.093816689
## M248_S_noaba_9-LA1511_S_noaba_9 -0.1246666667 -0.416260595 0.166927262
## M058_C_1aba_9-M058_C_10aba_9 -0.5610000000 -0.873750758 -0.248249242
## M058_C_noaba_9-M058_C_10aba_9 -0.4290000000 -0.712816689 -0.145183311
## M058_S_10aba_9-M058_C_10aba_9 -0.2835000000 -0.584533058 0.017533058
## M058_S_1aba_9-M058_C_10aba_9 -0.1180000000 -0.401816689 0.165816689
## M058_S_noaba_9-M058_C_10aba_9 -0.4300000000 -0.713816689 -0.146183311
## M248_C_10aba_9-M058_C_10aba_9 -0.6940000000 -0.977816689 -0.410183311
## M248_C_1aba_9-M058_C_10aba_9 -0.6381428571 -0.950893616 -0.325392099
## M248_C_noaba_9-M058_C_10aba_9 -0.3230000000 -0.606816689 -0.039183311
## M248_S_10aba_9-M058_C_10aba_9 -0.6165555556 -0.908149484 -0.324961627
## M248_S_1aba_9-M058_C_10aba_9 -0.6630000000 -0.946816689 -0.379183311
## M248_S_noaba_9-M058_C_10aba_9 -0.5976666667 -0.889260595 -0.306072738
## M058_C_noaba_9-M058_C_1aba_9 0.1320000000 -0.180750758 0.444750758
## M058_S_10aba_9-M058_C_1aba_9 0.2775000000 -0.050953994 0.605953994
## M058_S_1aba_9-M058_C_1aba_9 0.4430000000 0.130249242 0.755750758
## M058_S_noaba_9-M058_C_1aba_9 0.1310000000 -0.181750758 0.443750758
## M248_C_10aba_9-M058_C_1aba_9 -0.1330000000 -0.445750758 0.179750758
## M248_C_1aba_9-M058_C_1aba_9 -0.0771428571 -0.416368683 0.262082969
## M248_C_noaba_9-M058_C_1aba_9 0.2380000000 -0.074750758 0.550750758
## M248_S_10aba_9-M058_C_1aba_9 -0.0555555556 -0.375380731 0.264269620
## M248_S_1aba_9-M058_C_1aba_9 -0.1020000000 -0.414750758 0.210750758
## M248_S_noaba_9-M058_C_1aba_9 -0.0366666667 -0.356491843 0.283158509
## M058_S_10aba_9-M058_C_noaba_9 0.1455000000 -0.155533058 0.446533058
## M058_S_1aba_9-M058_C_noaba_9 0.3110000000 0.027183311 0.594816689
## M058_S_noaba_9-M058_C_noaba_9 -0.0010000000 -0.284816689 0.282816689
## M248_C_10aba_9-M058_C_noaba_9 -0.2650000000 -0.548816689 0.018816689
## M248_C_1aba_9-M058_C_noaba_9 -0.2091428571 -0.521893616 0.103607901
## M248_C_noaba_9-M058_C_noaba_9 0.1060000000 -0.177816689 0.389816689
## M248_S_10aba_9-M058_C_noaba_9 -0.1875555556 -0.479149484 0.104038373
## M248_S_1aba_9-M058_C_noaba_9 -0.2340000000 -0.517816689 0.049816689
## M248_S_noaba_9-M058_C_noaba_9 -0.1686666667 -0.460260595 0.122927262
## M058_S_1aba_9-M058_S_10aba_9 0.1655000000 -0.135533058 0.466533058
## M058_S_noaba_9-M058_S_10aba_9 -0.1465000000 -0.447533058 0.154533058
## M248_C_10aba_9-M058_S_10aba_9 -0.4105000000 -0.711533058 -0.109466942
## M248_C_1aba_9-M058_S_10aba_9 -0.3546428571 -0.683096851 -0.026188863
## M248_C_noaba_9-M058_S_10aba_9 -0.0395000000 -0.340533058 0.261533058
## M248_S_10aba_9-M058_S_10aba_9 -0.3330555556 -0.641431962 -0.024679149
## M248_S_1aba_9-M058_S_10aba_9 -0.3795000000 -0.680533058 -0.078466942
## M248_S_noaba_9-M058_S_10aba_9 -0.3141666667 -0.622543073 -0.005790260
## M058_S_noaba_9-M058_S_1aba_9 -0.3120000000 -0.595816689 -0.028183311
## M248_C_10aba_9-M058_S_1aba_9 -0.5760000000 -0.859816689 -0.292183311
## M248_C_1aba_9-M058_S_1aba_9 -0.5201428571 -0.832893616 -0.207392099
## M248_C_noaba_9-M058_S_1aba_9 -0.2050000000 -0.488816689 0.078816689
## M248_S_10aba_9-M058_S_1aba_9 -0.4985555556 -0.790149484 -0.206961627
## M248_S_1aba_9-M058_S_1aba_9 -0.5450000000 -0.828816689 -0.261183311
## M248_S_noaba_9-M058_S_1aba_9 -0.4796666667 -0.771260595 -0.188072738
## M248_C_10aba_9-M058_S_noaba_9 -0.2640000000 -0.547816689 0.019816689
## M248_C_1aba_9-M058_S_noaba_9 -0.2081428571 -0.520893616 0.104607901
## M248_C_noaba_9-M058_S_noaba_9 0.1070000000 -0.176816689 0.390816689
## M248_S_10aba_9-M058_S_noaba_9 -0.1865555556 -0.478149484 0.105038373
## M248_S_1aba_9-M058_S_noaba_9 -0.2330000000 -0.516816689 0.050816689
## M248_S_noaba_9-M058_S_noaba_9 -0.1676666667 -0.459260595 0.123927262
## M248_C_1aba_9-M248_C_10aba_9 0.0558571429 -0.256893616 0.368607901
## M248_C_noaba_9-M248_C_10aba_9 0.3710000000 0.087183311 0.654816689
## M248_S_10aba_9-M248_C_10aba_9 0.0774444444 -0.214149484 0.369038373
## M248_S_1aba_9-M248_C_10aba_9 0.0310000000 -0.252816689 0.314816689
## M248_S_noaba_9-M248_C_10aba_9 0.0963333333 -0.195260595 0.387927262
## M248_C_noaba_9-M248_C_1aba_9 0.3151428571 0.002392099 0.627893616
## M248_S_10aba_9-M248_C_1aba_9 0.0215873016 -0.298237874 0.341412478
## M248_S_1aba_9-M248_C_1aba_9 -0.0248571429 -0.337607901 0.287893616
## M248_S_noaba_9-M248_C_1aba_9 0.0404761905 -0.279348985 0.360301366
## M248_S_10aba_9-M248_C_noaba_9 -0.2935555556 -0.585149484 -0.001961627
## M248_S_1aba_9-M248_C_noaba_9 -0.3400000000 -0.623816689 -0.056183311
## M248_S_noaba_9-M248_C_noaba_9 -0.2746666667 -0.566260595 0.016927262
## M248_S_1aba_9-M248_S_10aba_9 -0.0464444444 -0.338038373 0.245149484
## M248_S_noaba_9-M248_S_10aba_9 0.0188888889 -0.280280169 0.318057947
## M248_S_noaba_9-M248_S_1aba_9 0.0653333333 -0.226260595 0.356927262
## p adj
## LA1511_C_1aba_9-LA1511_C_10aba_9 1.0000000
## LA1511_C_noaba_9-LA1511_C_10aba_9 0.9998687
## LA1511_S_10aba_9-LA1511_C_10aba_9 0.9939639
## LA1511_S_1aba_9-LA1511_C_10aba_9 0.9999970
## LA1511_S_noaba_9-LA1511_C_10aba_9 0.8241182
## M058_C_10aba_9-LA1511_C_10aba_9 0.0000000
## M058_C_1aba_9-LA1511_C_10aba_9 0.9999870
## M058_C_noaba_9-LA1511_C_10aba_9 0.4398915
## M058_S_10aba_9-LA1511_C_10aba_9 0.0057868
## M058_S_1aba_9-LA1511_C_10aba_9 0.0000002
## M058_S_noaba_9-LA1511_C_10aba_9 0.4488608
## M248_C_10aba_9-LA1511_C_10aba_9 0.9999997
## M248_C_1aba_9-LA1511_C_10aba_9 1.0000000
## M248_C_noaba_9-LA1511_C_10aba_9 0.0136132
## M248_S_10aba_9-LA1511_C_10aba_9 1.0000000
## M248_S_1aba_9-LA1511_C_10aba_9 1.0000000
## M248_S_noaba_9-LA1511_C_10aba_9 1.0000000
## LA1511_C_noaba_9-LA1511_C_1aba_9 0.9999980
## LA1511_S_10aba_9-LA1511_C_1aba_9 0.9993898
## LA1511_S_1aba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_1aba_9 0.9537007
## M058_C_10aba_9-LA1511_C_1aba_9 0.0000000
## M058_C_1aba_9-LA1511_C_1aba_9 0.9999999
## M058_C_noaba_9-LA1511_C_1aba_9 0.7057660
## M058_S_10aba_9-LA1511_C_1aba_9 0.0246410
## M058_S_1aba_9-LA1511_C_1aba_9 0.0000031
## M058_S_noaba_9-LA1511_C_1aba_9 0.7139177
## M248_C_10aba_9-LA1511_C_1aba_9 0.9999913
## M248_C_1aba_9-LA1511_C_1aba_9 1.0000000
## M248_C_noaba_9-LA1511_C_1aba_9 0.0556219
## M248_S_10aba_9-LA1511_C_1aba_9 1.0000000
## M248_S_1aba_9-LA1511_C_1aba_9 1.0000000
## M248_S_noaba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_10aba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_1aba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_noaba_9 0.9999476
## M058_C_10aba_9-LA1511_C_noaba_9 0.0000001
## M058_C_1aba_9-LA1511_C_noaba_9 1.0000000
## M058_C_noaba_9-LA1511_C_noaba_9 0.9883555
## M058_S_10aba_9-LA1511_C_noaba_9 0.1670790
## M058_S_1aba_9-LA1511_C_noaba_9 0.0000601
## M058_S_noaba_9-LA1511_C_noaba_9 0.9893007
## M248_C_10aba_9-LA1511_C_noaba_9 0.9606186
## M248_C_1aba_9-LA1511_C_noaba_9 0.9999681
## M248_C_noaba_9-LA1511_C_noaba_9 0.3217145
## M248_S_10aba_9-LA1511_C_noaba_9 0.9999988
## M248_S_1aba_9-LA1511_C_noaba_9 0.9970303
## M248_S_noaba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_1aba_9-LA1511_S_10aba_9 0.9999993
## LA1511_S_noaba_9-LA1511_S_10aba_9 1.0000000
## M058_C_10aba_9-LA1511_S_10aba_9 0.0000240
## M058_C_1aba_9-LA1511_S_10aba_9 1.0000000
## M058_C_noaba_9-LA1511_S_10aba_9 0.9999925
## M058_S_10aba_9-LA1511_S_10aba_9 0.6649187
## M058_S_1aba_9-LA1511_S_10aba_9 0.0052049
## M058_S_noaba_9-LA1511_S_10aba_9 0.9999938
## M248_C_10aba_9-LA1511_S_10aba_9 0.8545983
## M248_C_1aba_9-LA1511_S_10aba_9 0.9976121
## M248_C_noaba_9-LA1511_S_10aba_9 0.8634352
## M248_S_10aba_9-LA1511_S_10aba_9 0.9995001
## M248_S_1aba_9-LA1511_S_10aba_9 0.9667112
## M248_S_noaba_9-LA1511_S_10aba_9 0.9999616
## LA1511_S_noaba_9-LA1511_S_1aba_9 0.9982874
## M058_C_10aba_9-LA1511_S_1aba_9 0.0000000
## M058_C_1aba_9-LA1511_S_1aba_9 1.0000000
## M058_C_noaba_9-LA1511_S_1aba_9 0.9319173
## M058_S_10aba_9-LA1511_S_1aba_9 0.0695166
## M058_S_1aba_9-LA1511_S_1aba_9 0.0000086
## M058_S_noaba_9-LA1511_S_1aba_9 0.9356810
## M248_C_10aba_9-LA1511_S_1aba_9 0.9901499
## M248_C_1aba_9-LA1511_S_1aba_9 0.9999994
## M248_C_noaba_9-LA1511_S_1aba_9 0.1489953
## M248_S_10aba_9-LA1511_S_1aba_9 1.0000000
## M248_S_1aba_9-LA1511_S_1aba_9 0.9997348
## M248_S_noaba_9-LA1511_S_1aba_9 1.0000000
## M058_C_10aba_9-LA1511_S_noaba_9 0.0000033
## M058_C_1aba_9-LA1511_S_noaba_9 0.9999284
## M058_C_noaba_9-LA1511_S_noaba_9 1.0000000
## M058_S_10aba_9-LA1511_S_noaba_9 0.7259950
## M058_S_1aba_9-LA1511_S_noaba_9 0.0022583
## M058_S_noaba_9-LA1511_S_noaba_9 1.0000000
## M248_C_10aba_9-LA1511_S_noaba_9 0.3460716
## M248_C_1aba_9-LA1511_S_noaba_9 0.9159509
## M248_C_noaba_9-LA1511_S_noaba_9 0.9153504
## M248_S_10aba_9-LA1511_S_noaba_9 0.9531409
## M248_S_1aba_9-LA1511_S_noaba_9 0.6249638
## M248_S_noaba_9-LA1511_S_noaba_9 0.9879143
## M058_C_1aba_9-M058_C_10aba_9 0.0000003
## M058_C_noaba_9-M058_C_10aba_9 0.0000443
## M058_S_10aba_9-M058_C_10aba_9 0.0905283
## M058_S_1aba_9-M058_C_10aba_9 0.9909959
## M058_S_noaba_9-M058_C_10aba_9 0.0000418
## M248_C_10aba_9-M058_C_10aba_9 0.0000000
## M248_C_1aba_9-M058_C_10aba_9 0.0000000
## M248_C_noaba_9-M058_C_10aba_9 0.0100256
## M248_S_10aba_9-M058_C_10aba_9 0.0000000
## M248_S_1aba_9-M058_C_10aba_9 0.0000000
## M248_S_noaba_9-M058_C_10aba_9 0.0000000
## M058_C_noaba_9-M058_C_1aba_9 0.9894385
## M058_S_10aba_9-M058_C_1aba_9 0.2135791
## M058_S_1aba_9-M058_C_1aba_9 0.0001990
## M058_S_noaba_9-M058_C_1aba_9 0.9902542
## M248_C_10aba_9-M058_C_1aba_9 0.9885684
## M248_C_1aba_9-M058_C_1aba_9 0.9999966
## M248_C_noaba_9-M058_C_1aba_9 0.3876558
## M248_S_10aba_9-M058_C_1aba_9 0.9999999
## M248_S_1aba_9-M058_C_1aba_9 0.9994883
## M248_S_noaba_9-M058_C_1aba_9 1.0000000
## M058_S_10aba_9-M058_C_noaba_9 0.9602137
## M058_S_1aba_9-M058_C_noaba_9 0.0168570
## M058_S_noaba_9-M058_C_noaba_9 1.0000000
## M248_C_10aba_9-M058_C_noaba_9 0.0978459
## M248_C_1aba_9-M058_C_noaba_9 0.6268653
## M248_C_noaba_9-M058_C_noaba_9 0.9972947
## M248_S_10aba_9-M058_C_noaba_9 0.6923453
## M248_S_1aba_9-M058_C_noaba_9 0.2501758
## M248_S_noaba_9-M058_C_noaba_9 0.8365580
## M058_S_1aba_9-M058_S_10aba_9 0.8856388
## M058_S_noaba_9-M058_S_10aba_9 0.9576953
## M248_C_10aba_9-M058_S_10aba_9 0.0004440
## M248_C_1aba_9-M058_S_10aba_9 0.0204064
## M248_C_noaba_9-M058_S_10aba_9 1.0000000
## M248_S_10aba_9-M058_S_10aba_9 0.0203353
## M248_S_1aba_9-M058_S_10aba_9 0.0019693
## M248_S_noaba_9-M058_S_10aba_9 0.0408259
## M058_S_noaba_9-M058_S_1aba_9 0.0161569
## M248_C_10aba_9-M058_S_1aba_9 0.0000000
## M248_C_1aba_9-M058_S_1aba_9 0.0000035
## M248_C_noaba_9-M058_S_1aba_9 0.4852712
## M248_S_10aba_9-M058_S_1aba_9 0.0000016
## M248_S_1aba_9-M058_S_1aba_9 0.0000000
## M248_S_noaba_9-M058_S_1aba_9 0.0000048
## M248_C_10aba_9-M058_S_noaba_9 0.1011946
## M248_C_1aba_9-M058_S_noaba_9 0.6352237
## M248_C_noaba_9-M058_S_noaba_9 0.9969813
## M248_S_10aba_9-M058_S_noaba_9 0.7008838
## M248_S_1aba_9-M058_S_noaba_9 0.2568910
## M248_S_noaba_9-M058_S_noaba_9 0.8429659
## M248_C_1aba_9-M248_C_10aba_9 0.9999999
## M248_C_noaba_9-M248_C_10aba_9 0.0010177
## M248_S_10aba_9-M248_C_10aba_9 0.9999680
## M248_S_1aba_9-M248_C_10aba_9 1.0000000
## M248_S_noaba_9-M248_C_10aba_9 0.9993968
## M248_C_noaba_9-M248_C_1aba_9 0.0460669
## M248_S_10aba_9-M248_C_1aba_9 1.0000000
## M248_S_1aba_9-M248_C_1aba_9 1.0000000
## M248_S_noaba_9-M248_C_1aba_9 1.0000000
## M248_S_10aba_9-M248_C_noaba_9 0.0465260
## M248_S_1aba_9-M248_C_noaba_9 0.0046245
## M248_S_noaba_9-M248_C_noaba_9 0.0903594
## M248_S_1aba_9-M248_S_10aba_9 1.0000000
## M248_S_noaba_9-M248_S_10aba_9 1.0000000
## M248_S_noaba_9-M248_S_1aba_9 0.9999973
P6 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P6)
stat.test
## LA1511_C_1aba_9 LA1511_C_noaba_9 LA1511_S_10aba_9 LA1511_S_1aba_9
## "ab" "abc" "abc" "abc"
## LA1511_S_noaba_9 M058_C_10aba_9 M058_C_1aba_9 M058_C_noaba_9
## "abc" "d" "abc" "abc"
## M058_S_10aba_9 M058_S_1aba_9 M058_S_noaba_9 M248_C_10aba_9
## "cde" "de" "abc" "a"
## M248_C_1aba_9 M248_C_noaba_9 M248_S_10aba_9 M248_S_1aba_9
## "a" "bce" "a" "a"
## M248_S_noaba_9 LA1511_C_10aba_9
## "ab" "a"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ABA_pareto_location$Condition.all <- factor(ABA_pareto_location$Condition.all, levels = c("C_noaba", "C_1aba","C_10aba", "S_noaba","S_1aba","S_10aba"))
ABA_pareto_location_graph <- ggplot(data = ABA_pareto_location, mapping = aes(x = All.ID, y = pareto.front.scaling.location
, colour = Condition.all))
ABA_pareto_location_graph <- ABA_pareto_location_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_location_graph <- ABA_pareto_location_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_location_graph <- ABA_pareto_location_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_location_graph <- ABA_pareto_location_graph + ylab("Pareto front location") + xlab("") #+ ggtitle("")
ABA_pareto_location_graph <- ABA_pareto_location_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
ABA_pareto_location_graph <- ABA_pareto_location_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 1.5)
ABA_pareto_location_graph
ABA_pareto_location_graph <- ggplot(data=ABA_pareto_location, aes(x= Condition.all, y=pareto.front.scaling.location, color = Condition.all))
ABA_pareto_location_graph <- ABA_pareto_location_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_location_graph <- ABA_pareto_location_graph + facet_grid(~ Accessions )
ABA_pareto_location_graph <- ABA_pareto_location_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_location_graph <- ABA_pareto_location_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_location_graph <- ABA_pareto_location_graph + ylab("Pareto front scaling location") + xlab("") + theme(legend.position='none') + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
ABA_pareto_location_graph
aov(pareto.front.scaling.distance ~ All.ID, data = ABA_pareto_location)
## Call:
## aov(formula = pareto.front.scaling.distance ~ All.ID, data = ABA_pareto_location)
##
## Terms:
## All.ID Residuals
## Sum of Squares 3.554491 18.615125
## Deg. of Freedom 17 145
##
## Residual standard error: 0.3583018
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.scaling.distance ~ All.ID, data = ABA_pareto_location))
Output
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = pareto.front.scaling.distance ~ All.ID, data = ABA_pareto_location)
##
## $All.ID
## diff lwr upr
## LA1511_C_1aba_9-LA1511_C_10aba_9 -0.0278730750 -0.63170229 0.57595614
## LA1511_C_noaba_9-LA1511_C_10aba_9 -0.0317205889 -0.61661627 0.55317509
## LA1511_S_10aba_9-LA1511_C_10aba_9 -0.0070168667 -0.66438286 0.65034912
## LA1511_S_1aba_9-LA1511_C_10aba_9 -0.0096910000 -0.57898665 0.55960465
## LA1511_S_noaba_9-LA1511_C_10aba_9 -0.0314829000 -0.60077855 0.53781275
## M058_C_10aba_9-LA1511_C_10aba_9 0.4821732000 -0.08712245 1.05146885
## M058_C_1aba_9-LA1511_C_10aba_9 0.0963055857 -0.53102766 0.72363884
## M058_C_noaba_9-LA1511_C_10aba_9 -0.0087625000 -0.57805815 0.56053315
## M058_S_10aba_9-LA1511_C_10aba_9 0.0984076750 -0.50542154 0.70223689
## M058_S_1aba_9-LA1511_C_10aba_9 0.4298057000 -0.13948995 0.99910135
## M058_S_noaba_9-LA1511_C_10aba_9 0.0849756000 -0.48432005 0.65427125
## M248_C_10aba_9-LA1511_C_10aba_9 0.0142222000 -0.55507345 0.58351785
## M248_C_1aba_9-LA1511_C_10aba_9 0.0452025857 -0.58213066 0.67253584
## M248_C_noaba_9-LA1511_C_10aba_9 0.0567612000 -0.51253445 0.62605685
## M248_S_10aba_9-LA1511_C_10aba_9 0.0440681889 -0.54082749 0.62896387
## M248_S_1aba_9-LA1511_C_10aba_9 0.0274957000 -0.54179995 0.59679135
## M248_S_noaba_9-LA1511_C_10aba_9 0.0374659667 -0.54742971 0.62236164
## LA1511_C_noaba_9-LA1511_C_1aba_9 -0.0038475139 -0.62240644 0.61471141
## LA1511_S_10aba_9-LA1511_C_1aba_9 0.0208562083 -0.66663360 0.70834602
## LA1511_S_1aba_9-LA1511_C_1aba_9 0.0181820750 -0.58564714 0.62201129
## LA1511_S_noaba_9-LA1511_C_1aba_9 -0.0036098250 -0.60743904 0.60021939
## M058_C_10aba_9-LA1511_C_1aba_9 0.5100462750 -0.09378294 1.11387549
## M058_C_1aba_9-LA1511_C_1aba_9 0.1241786607 -0.53465303 0.78301035
## M058_C_noaba_9-LA1511_C_1aba_9 0.0191105750 -0.58471864 0.62293979
## M058_S_10aba_9-LA1511_C_1aba_9 0.1262807500 -0.51021113 0.76277263
## M058_S_1aba_9-LA1511_C_1aba_9 0.4576787750 -0.14615044 1.06150799
## M058_S_noaba_9-LA1511_C_1aba_9 0.1128486750 -0.49098054 0.71667789
## M248_C_10aba_9-LA1511_C_1aba_9 0.0420952750 -0.56173394 0.64592449
## M248_C_1aba_9-LA1511_C_1aba_9 0.0730756607 -0.58575603 0.73190735
## M248_C_noaba_9-LA1511_C_1aba_9 0.0846342750 -0.51919494 0.68846349
## M248_S_10aba_9-LA1511_C_1aba_9 0.0719412639 -0.54661766 0.69050019
## M248_S_1aba_9-LA1511_C_1aba_9 0.0553687750 -0.54846044 0.65919799
## M248_S_noaba_9-LA1511_C_1aba_9 0.0653390417 -0.55321988 0.68389797
## LA1511_S_10aba_9-LA1511_C_noaba_9 0.0247037222 -0.64621763 0.69562508
## LA1511_S_1aba_9-LA1511_C_noaba_9 0.0220295889 -0.56286609 0.60692527
## LA1511_S_noaba_9-LA1511_C_noaba_9 0.0002376889 -0.58465799 0.58513337
## M058_C_10aba_9-LA1511_C_noaba_9 0.5138937889 -0.07100189 1.09878947
## M058_C_1aba_9-LA1511_C_noaba_9 0.1280261746 -0.51349734 0.76954969
## M058_C_noaba_9-LA1511_C_noaba_9 0.0229580889 -0.56193759 0.60785377
## M058_S_10aba_9-LA1511_C_noaba_9 0.1301282639 -0.48843066 0.74868719
## M058_S_1aba_9-LA1511_C_noaba_9 0.4615262889 -0.12336939 1.04642197
## M058_S_noaba_9-LA1511_C_noaba_9 0.1166961889 -0.46819949 0.70159187
## M248_C_10aba_9-LA1511_C_noaba_9 0.0459427889 -0.53895289 0.63083847
## M248_C_1aba_9-LA1511_C_noaba_9 0.0769231746 -0.56460034 0.71844669
## M248_C_noaba_9-LA1511_C_noaba_9 0.0884817889 -0.49641389 0.67337747
## M248_S_10aba_9-LA1511_C_noaba_9 0.0757887778 -0.52430153 0.67587908
## M248_S_1aba_9-LA1511_C_noaba_9 0.0592162889 -0.52567939 0.64411197
## M248_S_noaba_9-LA1511_C_noaba_9 0.0691865556 -0.53090375 0.66927686
## LA1511_S_1aba_9-LA1511_S_10aba_9 -0.0026741333 -0.66004012 0.65469186
## LA1511_S_noaba_9-LA1511_S_10aba_9 -0.0244660333 -0.68183202 0.63289996
## M058_C_10aba_9-LA1511_S_10aba_9 0.4891900667 -0.16817592 1.14655606
## M058_C_1aba_9-LA1511_S_10aba_9 0.1033224524 -0.60490034 0.81154524
## M058_C_noaba_9-LA1511_S_10aba_9 -0.0017456333 -0.65911162 0.65562036
## M058_S_10aba_9-LA1511_S_10aba_9 0.1054245417 -0.58206527 0.79291435
## M058_S_1aba_9-LA1511_S_10aba_9 0.4368225667 -0.22054342 1.09418856
## M058_S_noaba_9-LA1511_S_10aba_9 0.0919924667 -0.56537352 0.74935846
## M248_C_10aba_9-LA1511_S_10aba_9 0.0212390667 -0.63612692 0.67860506
## M248_C_1aba_9-LA1511_S_10aba_9 0.0522194524 -0.65600334 0.76044224
## M248_C_noaba_9-LA1511_S_10aba_9 0.0637780667 -0.59358792 0.72114406
## M248_S_10aba_9-LA1511_S_10aba_9 0.0510850556 -0.61983630 0.72200641
## M248_S_1aba_9-LA1511_S_10aba_9 0.0345125667 -0.62285342 0.69187856
## M248_S_noaba_9-LA1511_S_10aba_9 0.0444828333 -0.62643852 0.71540419
## LA1511_S_noaba_9-LA1511_S_1aba_9 -0.0217919000 -0.59108755 0.54750375
## M058_C_10aba_9-LA1511_S_1aba_9 0.4918642000 -0.07743145 1.06115985
## M058_C_1aba_9-LA1511_S_1aba_9 0.1059965857 -0.52133666 0.73332984
## M058_C_noaba_9-LA1511_S_1aba_9 0.0009285000 -0.56836715 0.57022415
## M058_S_10aba_9-LA1511_S_1aba_9 0.1080986750 -0.49573054 0.71192789
## M058_S_1aba_9-LA1511_S_1aba_9 0.4394967000 -0.12979895 1.00879235
## M058_S_noaba_9-LA1511_S_1aba_9 0.0946666000 -0.47462905 0.66396225
## M248_C_10aba_9-LA1511_S_1aba_9 0.0239132000 -0.54538245 0.59320885
## M248_C_1aba_9-LA1511_S_1aba_9 0.0548935857 -0.57243966 0.68222684
## M248_C_noaba_9-LA1511_S_1aba_9 0.0664522000 -0.50284345 0.63574785
## M248_S_10aba_9-LA1511_S_1aba_9 0.0537591889 -0.53113649 0.63865487
## M248_S_1aba_9-LA1511_S_1aba_9 0.0371867000 -0.53210895 0.60648235
## M248_S_noaba_9-LA1511_S_1aba_9 0.0471569667 -0.53773871 0.63205264
## M058_C_10aba_9-LA1511_S_noaba_9 0.5136561000 -0.05563955 1.08295175
## M058_C_1aba_9-LA1511_S_noaba_9 0.1277884857 -0.49954476 0.75512174
## M058_C_noaba_9-LA1511_S_noaba_9 0.0227204000 -0.54657525 0.59201605
## M058_S_10aba_9-LA1511_S_noaba_9 0.1298905750 -0.47393864 0.73371979
## M058_S_1aba_9-LA1511_S_noaba_9 0.4612886000 -0.10800705 1.03058425
## M058_S_noaba_9-LA1511_S_noaba_9 0.1164585000 -0.45283715 0.68575415
## M248_C_10aba_9-LA1511_S_noaba_9 0.0457051000 -0.52359055 0.61500075
## M248_C_1aba_9-LA1511_S_noaba_9 0.0766854857 -0.55064776 0.70401874
## M248_C_noaba_9-LA1511_S_noaba_9 0.0882441000 -0.48105155 0.65753975
## M248_S_10aba_9-LA1511_S_noaba_9 0.0755510889 -0.50934459 0.66044677
## M248_S_1aba_9-LA1511_S_noaba_9 0.0589786000 -0.51031705 0.62827425
## M248_S_noaba_9-LA1511_S_noaba_9 0.0689488667 -0.51594681 0.65384454
## M058_C_1aba_9-M058_C_10aba_9 -0.3858676143 -1.01320086 0.24146564
## M058_C_noaba_9-M058_C_10aba_9 -0.4909357000 -1.06023135 0.07835995
## M058_S_10aba_9-M058_C_10aba_9 -0.3837655250 -0.98759474 0.22006369
## M058_S_1aba_9-M058_C_10aba_9 -0.0523675000 -0.62166315 0.51692815
## M058_S_noaba_9-M058_C_10aba_9 -0.3971976000 -0.96649325 0.17209805
## M248_C_10aba_9-M058_C_10aba_9 -0.4679510000 -1.03724665 0.10134465
## M248_C_1aba_9-M058_C_10aba_9 -0.4369706143 -1.06430386 0.19036264
## M248_C_noaba_9-M058_C_10aba_9 -0.4254120000 -0.99470765 0.14388365
## M248_S_10aba_9-M058_C_10aba_9 -0.4381050111 -1.02300069 0.14679067
## M248_S_1aba_9-M058_C_10aba_9 -0.4546775000 -1.02397315 0.11461815
## M248_S_noaba_9-M058_C_10aba_9 -0.4447072333 -1.02960291 0.14018844
## M058_C_noaba_9-M058_C_1aba_9 -0.1050680857 -0.73240134 0.52226516
## M058_S_10aba_9-M058_C_1aba_9 0.0021020893 -0.65672960 0.66093378
## M058_S_1aba_9-M058_C_1aba_9 0.3335001143 -0.29383314 0.96083336
## M058_S_noaba_9-M058_C_1aba_9 -0.0113299857 -0.63866324 0.61600326
## M248_C_10aba_9-M058_C_1aba_9 -0.0820833857 -0.70941664 0.54524986
## M248_C_1aba_9-M058_C_1aba_9 -0.0511030000 -0.73154145 0.62933545
## M248_C_noaba_9-M058_C_1aba_9 -0.0395443857 -0.66687764 0.58778886
## M248_S_10aba_9-M058_C_1aba_9 -0.0522373968 -0.69376092 0.58928612
## M248_S_1aba_9-M058_C_1aba_9 -0.0688098857 -0.69614314 0.55852336
## M248_S_noaba_9-M058_C_1aba_9 -0.0588396190 -0.70036314 0.58268390
## M058_S_10aba_9-M058_C_noaba_9 0.1071701750 -0.49665904 0.71099939
## M058_S_1aba_9-M058_C_noaba_9 0.4385682000 -0.13072745 1.00786385
## M058_S_noaba_9-M058_C_noaba_9 0.0937381000 -0.47555755 0.66303375
## M248_C_10aba_9-M058_C_noaba_9 0.0229847000 -0.54631095 0.59228035
## M248_C_1aba_9-M058_C_noaba_9 0.0539650857 -0.57336816 0.68129834
## M248_C_noaba_9-M058_C_noaba_9 0.0655237000 -0.50377195 0.63481935
## M248_S_10aba_9-M058_C_noaba_9 0.0528306889 -0.53206499 0.63772637
## M248_S_1aba_9-M058_C_noaba_9 0.0362582000 -0.53303745 0.60555385
## M248_S_noaba_9-M058_C_noaba_9 0.0462284667 -0.53866721 0.63112414
## M058_S_1aba_9-M058_S_10aba_9 0.3313980250 -0.27243119 0.93522724
## M058_S_noaba_9-M058_S_10aba_9 -0.0134320750 -0.61726129 0.59039714
## M248_C_10aba_9-M058_S_10aba_9 -0.0841854750 -0.68801469 0.51964374
## M248_C_1aba_9-M058_S_10aba_9 -0.0532050893 -0.71203678 0.60562660
## M248_C_noaba_9-M058_S_10aba_9 -0.0416464750 -0.64547569 0.56218274
## M248_S_10aba_9-M058_S_10aba_9 -0.0543394861 -0.67289841 0.56421944
## M248_S_1aba_9-M058_S_10aba_9 -0.0709119750 -0.67474119 0.53291724
## M248_S_noaba_9-M058_S_10aba_9 -0.0609417083 -0.67950063 0.55761722
## M058_S_noaba_9-M058_S_1aba_9 -0.3448301000 -0.91412575 0.22446555
## M248_C_10aba_9-M058_S_1aba_9 -0.4155835000 -0.98487915 0.15371215
## M248_C_1aba_9-M058_S_1aba_9 -0.3846031143 -1.01193636 0.24273014
## M248_C_noaba_9-M058_S_1aba_9 -0.3730445000 -0.94234015 0.19625115
## M248_S_10aba_9-M058_S_1aba_9 -0.3857375111 -0.97063319 0.19915817
## M248_S_1aba_9-M058_S_1aba_9 -0.4023100000 -0.97160565 0.16698565
## M248_S_noaba_9-M058_S_1aba_9 -0.3923397333 -0.97723541 0.19255594
## M248_C_10aba_9-M058_S_noaba_9 -0.0707534000 -0.64004905 0.49854225
## M248_C_1aba_9-M058_S_noaba_9 -0.0397730143 -0.66710626 0.58756024
## M248_C_noaba_9-M058_S_noaba_9 -0.0282144000 -0.59751005 0.54108125
## M248_S_10aba_9-M058_S_noaba_9 -0.0409074111 -0.62580309 0.54398827
## M248_S_1aba_9-M058_S_noaba_9 -0.0574799000 -0.62677555 0.51181575
## M248_S_noaba_9-M058_S_noaba_9 -0.0475096333 -0.63240531 0.53738604
## M248_C_1aba_9-M248_C_10aba_9 0.0309803857 -0.59635286 0.65831364
## M248_C_noaba_9-M248_C_10aba_9 0.0425390000 -0.52675665 0.61183465
## M248_S_10aba_9-M248_C_10aba_9 0.0298459889 -0.55504969 0.61474167
## M248_S_1aba_9-M248_C_10aba_9 0.0132735000 -0.55602215 0.58256915
## M248_S_noaba_9-M248_C_10aba_9 0.0232437667 -0.56165191 0.60813944
## M248_C_noaba_9-M248_C_1aba_9 0.0115586143 -0.61577464 0.63889186
## M248_S_10aba_9-M248_C_1aba_9 -0.0011343968 -0.64265792 0.64038912
## M248_S_1aba_9-M248_C_1aba_9 -0.0177068857 -0.64504014 0.60962636
## M248_S_noaba_9-M248_C_1aba_9 -0.0077366190 -0.64926014 0.63378690
## M248_S_10aba_9-M248_C_noaba_9 -0.0126930111 -0.59758869 0.57220267
## M248_S_1aba_9-M248_C_noaba_9 -0.0292655000 -0.59856115 0.54003015
## M248_S_noaba_9-M248_C_noaba_9 -0.0192952333 -0.60419091 0.56560044
## M248_S_1aba_9-M248_S_10aba_9 -0.0165724889 -0.60146817 0.56832319
## M248_S_noaba_9-M248_S_10aba_9 -0.0066022222 -0.60669253 0.59348808
## M248_S_noaba_9-M248_S_1aba_9 0.0099702667 -0.57492541 0.59486594
## p adj
## LA1511_C_1aba_9-LA1511_C_10aba_9 1.0000000
## LA1511_C_noaba_9-LA1511_C_10aba_9 1.0000000
## LA1511_S_10aba_9-LA1511_C_10aba_9 1.0000000
## LA1511_S_1aba_9-LA1511_C_10aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_10aba_9 1.0000000
## M058_C_10aba_9-LA1511_C_10aba_9 0.2100354
## M058_C_1aba_9-LA1511_C_10aba_9 1.0000000
## M058_C_noaba_9-LA1511_C_10aba_9 1.0000000
## M058_S_10aba_9-LA1511_C_10aba_9 1.0000000
## M058_S_1aba_9-LA1511_C_10aba_9 0.4022850
## M058_S_noaba_9-LA1511_C_10aba_9 1.0000000
## M248_C_10aba_9-LA1511_C_10aba_9 1.0000000
## M248_C_1aba_9-LA1511_C_10aba_9 1.0000000
## M248_C_noaba_9-LA1511_C_10aba_9 1.0000000
## M248_S_10aba_9-LA1511_C_10aba_9 1.0000000
## M248_S_1aba_9-LA1511_C_10aba_9 1.0000000
## M248_S_noaba_9-LA1511_C_10aba_9 1.0000000
## LA1511_C_noaba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_10aba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_1aba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_1aba_9 1.0000000
## M058_C_10aba_9-LA1511_C_1aba_9 0.2138866
## M058_C_1aba_9-LA1511_C_1aba_9 0.9999998
## M058_C_noaba_9-LA1511_C_1aba_9 1.0000000
## M058_S_10aba_9-LA1511_C_1aba_9 0.9999996
## M058_S_1aba_9-LA1511_C_1aba_9 0.3949974
## M058_S_noaba_9-LA1511_C_1aba_9 0.9999998
## M248_C_10aba_9-LA1511_C_1aba_9 1.0000000
## M248_C_1aba_9-LA1511_C_1aba_9 1.0000000
## M248_C_noaba_9-LA1511_C_1aba_9 1.0000000
## M248_S_10aba_9-LA1511_C_1aba_9 1.0000000
## M248_S_1aba_9-LA1511_C_1aba_9 1.0000000
## M248_S_noaba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_10aba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_1aba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_noaba_9 1.0000000
## M058_C_10aba_9-LA1511_C_noaba_9 0.1615153
## M058_C_1aba_9-LA1511_C_noaba_9 0.9999995
## M058_C_noaba_9-LA1511_C_noaba_9 1.0000000
## M058_S_10aba_9-LA1511_C_noaba_9 0.9999990
## M058_S_1aba_9-LA1511_C_noaba_9 0.3227175
## M058_S_noaba_9-LA1511_C_noaba_9 0.9999995
## M248_C_10aba_9-LA1511_C_noaba_9 1.0000000
## M248_C_1aba_9-LA1511_C_noaba_9 1.0000000
## M248_C_noaba_9-LA1511_C_noaba_9 1.0000000
## M248_S_10aba_9-LA1511_C_noaba_9 1.0000000
## M248_S_1aba_9-LA1511_C_noaba_9 1.0000000
## M248_S_noaba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_1aba_9-LA1511_S_10aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_S_10aba_9 1.0000000
## M058_C_10aba_9-LA1511_S_10aba_9 0.4291478
## M058_C_1aba_9-LA1511_S_10aba_9 1.0000000
## M058_C_noaba_9-LA1511_S_10aba_9 1.0000000
## M058_S_10aba_9-LA1511_S_10aba_9 1.0000000
## M058_S_1aba_9-LA1511_S_10aba_9 0.6378796
## M058_S_noaba_9-LA1511_S_10aba_9 1.0000000
## M248_C_10aba_9-LA1511_S_10aba_9 1.0000000
## M248_C_1aba_9-LA1511_S_10aba_9 1.0000000
## M248_C_noaba_9-LA1511_S_10aba_9 1.0000000
## M248_S_10aba_9-LA1511_S_10aba_9 1.0000000
## M248_S_1aba_9-LA1511_S_10aba_9 1.0000000
## M248_S_noaba_9-LA1511_S_10aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_S_1aba_9 1.0000000
## M058_C_10aba_9-LA1511_S_1aba_9 0.1827889
## M058_C_1aba_9-LA1511_S_1aba_9 1.0000000
## M058_C_noaba_9-LA1511_S_1aba_9 1.0000000
## M058_S_10aba_9-LA1511_S_1aba_9 0.9999999
## M058_S_1aba_9-LA1511_S_1aba_9 0.3614923
## M058_S_noaba_9-LA1511_S_1aba_9 1.0000000
## M248_C_10aba_9-LA1511_S_1aba_9 1.0000000
## M248_C_1aba_9-LA1511_S_1aba_9 1.0000000
## M248_C_noaba_9-LA1511_S_1aba_9 1.0000000
## M248_S_10aba_9-LA1511_S_1aba_9 1.0000000
## M248_S_1aba_9-LA1511_S_1aba_9 1.0000000
## M248_S_noaba_9-LA1511_S_1aba_9 1.0000000
## M058_C_10aba_9-LA1511_S_noaba_9 0.1311059
## M058_C_1aba_9-LA1511_S_noaba_9 0.9999994
## M058_C_noaba_9-LA1511_S_noaba_9 1.0000000
## M058_S_10aba_9-LA1511_S_noaba_9 0.9999985
## M058_S_1aba_9-LA1511_S_noaba_9 0.2779260
## M058_S_noaba_9-LA1511_S_noaba_9 0.9999993
## M248_C_10aba_9-LA1511_S_noaba_9 1.0000000
## M248_C_1aba_9-LA1511_S_noaba_9 1.0000000
## M248_C_noaba_9-LA1511_S_noaba_9 1.0000000
## M248_S_10aba_9-LA1511_S_noaba_9 1.0000000
## M248_S_1aba_9-LA1511_S_noaba_9 1.0000000
## M248_S_noaba_9-LA1511_S_noaba_9 1.0000000
## M058_C_1aba_9-M058_C_10aba_9 0.7597858
## M058_C_noaba_9-M058_C_10aba_9 0.1852831
## M058_S_10aba_9-M058_C_10aba_9 0.7112973
## M058_S_1aba_9-M058_C_10aba_9 1.0000000
## M058_S_noaba_9-M058_C_10aba_9 0.5501743
## M248_C_10aba_9-M058_C_10aba_9 0.2549162
## M248_C_1aba_9-M058_C_10aba_9 0.5532226
## M248_C_noaba_9-M058_C_10aba_9 0.4213935
## M248_S_10aba_9-M058_C_10aba_9 0.4169784
## M248_S_1aba_9-M058_C_10aba_9 0.3019738
## M248_S_noaba_9-M058_C_10aba_9 0.3892758
## M058_C_noaba_9-M058_C_1aba_9 1.0000000
## M058_S_10aba_9-M058_C_1aba_9 1.0000000
## M058_S_1aba_9-M058_C_1aba_9 0.9113683
## M058_S_noaba_9-M058_C_1aba_9 1.0000000
## M248_C_10aba_9-M058_C_1aba_9 1.0000000
## M248_C_1aba_9-M058_C_1aba_9 1.0000000
## M248_C_noaba_9-M058_C_1aba_9 1.0000000
## M248_S_10aba_9-M058_C_1aba_9 1.0000000
## M248_S_1aba_9-M058_C_1aba_9 1.0000000
## M248_S_noaba_9-M058_C_1aba_9 1.0000000
## M058_S_10aba_9-M058_C_noaba_9 0.9999999
## M058_S_1aba_9-M058_C_noaba_9 0.3653131
## M058_S_noaba_9-M058_C_noaba_9 1.0000000
## M248_C_10aba_9-M058_C_noaba_9 1.0000000
## M248_C_1aba_9-M058_C_noaba_9 1.0000000
## M248_C_noaba_9-M058_C_noaba_9 1.0000000
## M248_S_10aba_9-M058_C_noaba_9 1.0000000
## M248_S_1aba_9-M058_C_noaba_9 1.0000000
## M248_S_noaba_9-M058_C_noaba_9 1.0000000
## M058_S_1aba_9-M058_S_10aba_9 0.8870830
## M058_S_noaba_9-M058_S_10aba_9 1.0000000
## M248_C_10aba_9-M058_S_10aba_9 1.0000000
## M248_C_1aba_9-M058_S_10aba_9 1.0000000
## M248_C_noaba_9-M058_S_10aba_9 1.0000000
## M248_S_10aba_9-M058_S_10aba_9 1.0000000
## M248_S_1aba_9-M058_S_10aba_9 1.0000000
## M248_S_noaba_9-M058_S_10aba_9 1.0000000
## M058_S_noaba_9-M058_S_1aba_9 0.7807722
## M248_C_10aba_9-M058_S_1aba_9 0.4652839
## M248_C_1aba_9-M058_S_1aba_9 0.7643675
## M248_C_noaba_9-M058_S_1aba_9 0.6617573
## M248_S_10aba_9-M058_S_1aba_9 0.6508744
## M248_S_1aba_9-M058_S_1aba_9 0.5263541
## M248_S_noaba_9-M058_S_1aba_9 0.6214494
## M248_C_10aba_9-M058_S_noaba_9 1.0000000
## M248_C_1aba_9-M058_S_noaba_9 1.0000000
## M248_C_noaba_9-M058_S_noaba_9 1.0000000
## M248_S_10aba_9-M058_S_noaba_9 1.0000000
## M248_S_1aba_9-M058_S_noaba_9 1.0000000
## M248_S_noaba_9-M058_S_noaba_9 1.0000000
## M248_C_1aba_9-M248_C_10aba_9 1.0000000
## M248_C_noaba_9-M248_C_10aba_9 1.0000000
## M248_S_10aba_9-M248_C_10aba_9 1.0000000
## M248_S_1aba_9-M248_C_10aba_9 1.0000000
## M248_S_noaba_9-M248_C_10aba_9 1.0000000
## M248_C_noaba_9-M248_C_1aba_9 1.0000000
## M248_S_10aba_9-M248_C_1aba_9 1.0000000
## M248_S_1aba_9-M248_C_1aba_9 1.0000000
## M248_S_noaba_9-M248_C_1aba_9 1.0000000
## M248_S_10aba_9-M248_C_noaba_9 1.0000000
## M248_S_1aba_9-M248_C_noaba_9 1.0000000
## M248_S_noaba_9-M248_C_noaba_9 1.0000000
## M248_S_1aba_9-M248_S_10aba_9 1.0000000
## M248_S_noaba_9-M248_S_10aba_9 1.0000000
## M248_S_noaba_9-M248_S_1aba_9 1.0000000
P5 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P5)
stat.test
## $Letters
## LA1511_C_1aba_9 LA1511_C_noaba_9 LA1511_S_10aba_9 LA1511_S_1aba_9
## "a" "a" "a" "a"
## LA1511_S_noaba_9 M058_C_10aba_9 M058_C_1aba_9 M058_C_noaba_9
## "a" "a" "a" "a"
## M058_S_10aba_9 M058_S_1aba_9 M058_S_noaba_9 M248_C_10aba_9
## "a" "a" "a" "a"
## M248_C_1aba_9 M248_C_noaba_9 M248_S_10aba_9 M248_S_1aba_9
## "a" "a" "a" "a"
## M248_S_noaba_9 LA1511_C_10aba_9
## "a" "a"
##
## $LetterMatrix
## a
## LA1511_C_1aba_9 TRUE
## LA1511_C_noaba_9 TRUE
## LA1511_S_10aba_9 TRUE
## LA1511_S_1aba_9 TRUE
## LA1511_S_noaba_9 TRUE
## M058_C_10aba_9 TRUE
## M058_C_1aba_9 TRUE
## M058_C_noaba_9 TRUE
## M058_S_10aba_9 TRUE
## M058_S_1aba_9 TRUE
## M058_S_noaba_9 TRUE
## M248_C_10aba_9 TRUE
## M248_C_1aba_9 TRUE
## M248_C_noaba_9 TRUE
## M248_S_10aba_9 TRUE
## M248_S_1aba_9 TRUE
## M248_S_noaba_9 TRUE
## LA1511_C_10aba_9 TRUE
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ABA_pareto_location2 <- subset(ABA_pareto_location, ABA_pareto_location$pareto.front.scaling.distanc < 3)
ABA_pareto_location2$Condition.all <- factor(ABA_pareto_location2$Condition.all, levels = c("C_noaba", "C_1aba","C_10aba", "S_noaba","S_1aba","S_10aba"))
ABA_pareto_distance_graph <- ggplot(data = ABA_pareto_location2, mapping = aes(x = All.ID, y = pareto.front.scaling.distance
, colour = Condition.all))
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + ylab("Pareto front scaling distance") + xlab("") #+ ggtitle("")
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 2.5)
ABA_pareto_distance_graph
ABA_pareto_distance_graph <- ggplot(data=ABA_pareto_location2, aes(x= Condition.all, y=pareto.front.scaling.distance, color = Condition.all))
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + facet_grid(~ Accessions )
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_distance_graph <- ABA_pareto_distance_graph + ylab("Pareto front scaling distance") + xlab("") + theme(legend.position='none') + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
ABA_pareto_distance_graph
next calculate for non-scaling values as well……..
aov(pareto.front.nonscaling.location ~ All.ID, data = ABA_pareto_location)
## Call:
## aov(formula = pareto.front.nonscaling.location ~ All.ID, data = ABA_pareto_location)
##
## Terms:
## All.ID Residuals
## Sum of Squares 4.612976 16.300055
## Deg. of Freedom 17 145
##
## Residual standard error: 0.3352822
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.nonscaling.location ~ All.ID, data = ABA_pareto_location))
Output
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = pareto.front.nonscaling.location ~ All.ID, data = ABA_pareto_location)
##
## $All.ID
## diff lwr upr
## LA1511_C_1aba_9-LA1511_C_10aba_9 0.101500000 -0.46353544 0.666535437
## LA1511_C_noaba_9-LA1511_C_10aba_9 0.045111111 -0.50220719 0.592429415
## LA1511_S_10aba_9-LA1511_C_10aba_9 -0.117666667 -0.73279934 0.497466003
## LA1511_S_1aba_9-LA1511_C_10aba_9 0.096000000 -0.43672052 0.628720519
## LA1511_S_noaba_9-LA1511_C_10aba_9 0.132000000 -0.40072052 0.664720519
## M058_C_10aba_9-LA1511_C_10aba_9 0.228000000 -0.30472052 0.760720519
## M058_C_1aba_9-LA1511_C_10aba_9 0.111142857 -0.47588656 0.698172278
## M058_C_noaba_9-LA1511_C_10aba_9 0.211000000 -0.32172052 0.743720519
## M058_S_10aba_9-LA1511_C_10aba_9 -0.182250000 -0.74728544 0.382785437
## M058_S_1aba_9-LA1511_C_10aba_9 0.139000000 -0.39372052 0.671720519
## M058_S_noaba_9-LA1511_C_10aba_9 -0.057000000 -0.58972052 0.475720519
## M248_C_10aba_9-LA1511_C_10aba_9 -0.204000000 -0.73672052 0.328720519
## M248_C_1aba_9-LA1511_C_10aba_9 -0.150285714 -0.73731513 0.436743706
## M248_C_noaba_9-LA1511_C_10aba_9 0.414000000 -0.11872052 0.946720519
## M248_S_10aba_9-LA1511_C_10aba_9 -0.091555556 -0.63887386 0.455762749
## M248_S_1aba_9-LA1511_C_10aba_9 -0.159000000 -0.69172052 0.373720519
## M248_S_noaba_9-LA1511_C_10aba_9 -0.127111111 -0.67442942 0.420207193
## LA1511_C_noaba_9-LA1511_C_1aba_9 -0.056388889 -0.63520770 0.522429926
## LA1511_S_10aba_9-LA1511_C_1aba_9 -0.219166667 -0.86248781 0.424154478
## LA1511_S_1aba_9-LA1511_C_1aba_9 -0.005500000 -0.57053544 0.559535437
## LA1511_S_noaba_9-LA1511_C_1aba_9 0.030500000 -0.53453544 0.595535437
## M058_C_10aba_9-LA1511_C_1aba_9 0.126500000 -0.43853544 0.691535437
## M058_C_1aba_9-LA1511_C_1aba_9 0.009642857 -0.60686135 0.626147062
## M058_C_noaba_9-LA1511_C_1aba_9 0.109500000 -0.45553544 0.674535437
## M058_S_10aba_9-LA1511_C_1aba_9 -0.283750000 -0.87934965 0.311849646
## M058_S_1aba_9-LA1511_C_1aba_9 0.037500000 -0.52753544 0.602535437
## M058_S_noaba_9-LA1511_C_1aba_9 -0.158500000 -0.72353544 0.406535437
## M248_C_10aba_9-LA1511_C_1aba_9 -0.305500000 -0.87053544 0.259535437
## M248_C_1aba_9-LA1511_C_1aba_9 -0.251785714 -0.86828992 0.364718491
## M248_C_noaba_9-LA1511_C_1aba_9 0.312500000 -0.25253544 0.877535437
## M248_S_10aba_9-LA1511_C_1aba_9 -0.193055556 -0.77187437 0.385763259
## M248_S_1aba_9-LA1511_C_1aba_9 -0.260500000 -0.82553544 0.304535437
## M248_S_noaba_9-LA1511_C_1aba_9 -0.228611111 -0.80742993 0.350207703
## LA1511_S_10aba_9-LA1511_C_noaba_9 -0.162777778 -0.79059493 0.465039374
## LA1511_S_1aba_9-LA1511_C_noaba_9 0.050888889 -0.49642942 0.598207193
## LA1511_S_noaba_9-LA1511_C_noaba_9 0.086888889 -0.46042942 0.634207193
## M058_C_10aba_9-LA1511_C_noaba_9 0.182888889 -0.36442942 0.730207193
## M058_C_1aba_9-LA1511_C_noaba_9 0.066031746 -0.53427627 0.666339763
## M058_C_noaba_9-LA1511_C_noaba_9 0.165888889 -0.38142942 0.713207193
## M058_S_10aba_9-LA1511_C_noaba_9 -0.227361111 -0.80617993 0.351457703
## M058_S_1aba_9-LA1511_C_noaba_9 0.093888889 -0.45342942 0.641207193
## M058_S_noaba_9-LA1511_C_noaba_9 -0.102111111 -0.64942942 0.445207193
## M248_C_10aba_9-LA1511_C_noaba_9 -0.249111111 -0.79642942 0.298207193
## M248_C_1aba_9-LA1511_C_noaba_9 -0.195396825 -0.79570484 0.404911192
## M248_C_noaba_9-LA1511_C_noaba_9 0.368888889 -0.17842942 0.916207193
## M248_S_10aba_9-LA1511_C_noaba_9 -0.136666667 -0.69820340 0.424870065
## M248_S_1aba_9-LA1511_C_noaba_9 -0.204111111 -0.75142942 0.343207193
## M248_S_noaba_9-LA1511_C_noaba_9 -0.172222222 -0.73375895 0.389314510
## LA1511_S_1aba_9-LA1511_S_10aba_9 0.213666667 -0.40146600 0.828799336
## LA1511_S_noaba_9-LA1511_S_10aba_9 0.249666667 -0.36546600 0.864799336
## M058_C_10aba_9-LA1511_S_10aba_9 0.345666667 -0.26946600 0.960799336
## M058_C_1aba_9-LA1511_S_10aba_9 0.228809524 -0.43391258 0.891531631
## M058_C_noaba_9-LA1511_S_10aba_9 0.328666667 -0.28646600 0.943799336
## M058_S_10aba_9-LA1511_S_10aba_9 -0.064583333 -0.70790448 0.578737811
## M058_S_1aba_9-LA1511_S_10aba_9 0.256666667 -0.35846600 0.871799336
## M058_S_noaba_9-LA1511_S_10aba_9 0.060666667 -0.55446600 0.675799336
## M248_C_10aba_9-LA1511_S_10aba_9 -0.086333333 -0.70146600 0.528799336
## M248_C_1aba_9-LA1511_S_10aba_9 -0.032619048 -0.69534115 0.630103059
## M248_C_noaba_9-LA1511_S_10aba_9 0.531666667 -0.08346600 1.146799336
## M248_S_10aba_9-LA1511_S_10aba_9 0.026111111 -0.60170604 0.653928263
## M248_S_1aba_9-LA1511_S_10aba_9 -0.041333333 -0.65646600 0.573799336
## M248_S_noaba_9-LA1511_S_10aba_9 -0.009444444 -0.63726160 0.618372708
## LA1511_S_noaba_9-LA1511_S_1aba_9 0.036000000 -0.49672052 0.568720519
## M058_C_10aba_9-LA1511_S_1aba_9 0.132000000 -0.40072052 0.664720519
## M058_C_1aba_9-LA1511_S_1aba_9 0.015142857 -0.57188656 0.602172278
## M058_C_noaba_9-LA1511_S_1aba_9 0.115000000 -0.41772052 0.647720519
## M058_S_10aba_9-LA1511_S_1aba_9 -0.278250000 -0.84328544 0.286785437
## M058_S_1aba_9-LA1511_S_1aba_9 0.043000000 -0.48972052 0.575720519
## M058_S_noaba_9-LA1511_S_1aba_9 -0.153000000 -0.68572052 0.379720519
## M248_C_10aba_9-LA1511_S_1aba_9 -0.300000000 -0.83272052 0.232720519
## M248_C_1aba_9-LA1511_S_1aba_9 -0.246285714 -0.83331513 0.340743706
## M248_C_noaba_9-LA1511_S_1aba_9 0.318000000 -0.21472052 0.850720519
## M248_S_10aba_9-LA1511_S_1aba_9 -0.187555556 -0.73487386 0.359762749
## M248_S_1aba_9-LA1511_S_1aba_9 -0.255000000 -0.78772052 0.277720519
## M248_S_noaba_9-LA1511_S_1aba_9 -0.223111111 -0.77042942 0.324207193
## M058_C_10aba_9-LA1511_S_noaba_9 0.096000000 -0.43672052 0.628720519
## M058_C_1aba_9-LA1511_S_noaba_9 -0.020857143 -0.60788656 0.566172278
## M058_C_noaba_9-LA1511_S_noaba_9 0.079000000 -0.45372052 0.611720519
## M058_S_10aba_9-LA1511_S_noaba_9 -0.314250000 -0.87928544 0.250785437
## M058_S_1aba_9-LA1511_S_noaba_9 0.007000000 -0.52572052 0.539720519
## M058_S_noaba_9-LA1511_S_noaba_9 -0.189000000 -0.72172052 0.343720519
## M248_C_10aba_9-LA1511_S_noaba_9 -0.336000000 -0.86872052 0.196720519
## M248_C_1aba_9-LA1511_S_noaba_9 -0.282285714 -0.86931513 0.304743706
## M248_C_noaba_9-LA1511_S_noaba_9 0.282000000 -0.25072052 0.814720519
## M248_S_10aba_9-LA1511_S_noaba_9 -0.223555556 -0.77087386 0.323762749
## M248_S_1aba_9-LA1511_S_noaba_9 -0.291000000 -0.82372052 0.241720519
## M248_S_noaba_9-LA1511_S_noaba_9 -0.259111111 -0.80642942 0.288207193
## M058_C_1aba_9-M058_C_10aba_9 -0.116857143 -0.70388656 0.470172278
## M058_C_noaba_9-M058_C_10aba_9 -0.017000000 -0.54972052 0.515720519
## M058_S_10aba_9-M058_C_10aba_9 -0.410250000 -0.97528544 0.154785437
## M058_S_1aba_9-M058_C_10aba_9 -0.089000000 -0.62172052 0.443720519
## M058_S_noaba_9-M058_C_10aba_9 -0.285000000 -0.81772052 0.247720519
## M248_C_10aba_9-M058_C_10aba_9 -0.432000000 -0.96472052 0.100720519
## M248_C_1aba_9-M058_C_10aba_9 -0.378285714 -0.96531513 0.208743706
## M248_C_noaba_9-M058_C_10aba_9 0.186000000 -0.34672052 0.718720519
## M248_S_10aba_9-M058_C_10aba_9 -0.319555556 -0.86687386 0.227762749
## M248_S_1aba_9-M058_C_10aba_9 -0.387000000 -0.91972052 0.145720519
## M248_S_noaba_9-M058_C_10aba_9 -0.355111111 -0.90242942 0.192207193
## M058_C_noaba_9-M058_C_1aba_9 0.099857143 -0.48717228 0.686886563
## M058_S_10aba_9-M058_C_1aba_9 -0.293392857 -0.90989706 0.323111348
## M058_S_1aba_9-M058_C_1aba_9 0.027857143 -0.55917228 0.614886563
## M058_S_noaba_9-M058_C_1aba_9 -0.168142857 -0.75517228 0.418886563
## M248_C_10aba_9-M058_C_1aba_9 -0.315142857 -0.90217228 0.271886563
## M248_C_1aba_9-M058_C_1aba_9 -0.261428571 -0.89815138 0.375294233
## M248_C_noaba_9-M058_C_1aba_9 0.302857143 -0.28417228 0.889886563
## M248_S_10aba_9-M058_C_1aba_9 -0.202698413 -0.80300643 0.397609605
## M248_S_1aba_9-M058_C_1aba_9 -0.270142857 -0.85717228 0.316886563
## M248_S_noaba_9-M058_C_1aba_9 -0.238253968 -0.83856199 0.362054049
## M058_S_10aba_9-M058_C_noaba_9 -0.393250000 -0.95828544 0.171785437
## M058_S_1aba_9-M058_C_noaba_9 -0.072000000 -0.60472052 0.460720519
## M058_S_noaba_9-M058_C_noaba_9 -0.268000000 -0.80072052 0.264720519
## M248_C_10aba_9-M058_C_noaba_9 -0.415000000 -0.94772052 0.117720519
## M248_C_1aba_9-M058_C_noaba_9 -0.361285714 -0.94831513 0.225743706
## M248_C_noaba_9-M058_C_noaba_9 0.203000000 -0.32972052 0.735720519
## M248_S_10aba_9-M058_C_noaba_9 -0.302555556 -0.84987386 0.244762749
## M248_S_1aba_9-M058_C_noaba_9 -0.370000000 -0.90272052 0.162720519
## M248_S_noaba_9-M058_C_noaba_9 -0.338111111 -0.88542942 0.209207193
## M058_S_1aba_9-M058_S_10aba_9 0.321250000 -0.24378544 0.886285437
## M058_S_noaba_9-M058_S_10aba_9 0.125250000 -0.43978544 0.690285437
## M248_C_10aba_9-M058_S_10aba_9 -0.021750000 -0.58678544 0.543285437
## M248_C_1aba_9-M058_S_10aba_9 0.031964286 -0.58453992 0.648468491
## M248_C_noaba_9-M058_S_10aba_9 0.596250000 0.03121456 1.161285437
## M248_S_10aba_9-M058_S_10aba_9 0.090694444 -0.48812437 0.669513259
## M248_S_1aba_9-M058_S_10aba_9 0.023250000 -0.54178544 0.588285437
## M248_S_noaba_9-M058_S_10aba_9 0.055138889 -0.52367993 0.633957703
## M058_S_noaba_9-M058_S_1aba_9 -0.196000000 -0.72872052 0.336720519
## M248_C_10aba_9-M058_S_1aba_9 -0.343000000 -0.87572052 0.189720519
## M248_C_1aba_9-M058_S_1aba_9 -0.289285714 -0.87631513 0.297743706
## M248_C_noaba_9-M058_S_1aba_9 0.275000000 -0.25772052 0.807720519
## M248_S_10aba_9-M058_S_1aba_9 -0.230555556 -0.77787386 0.316762749
## M248_S_1aba_9-M058_S_1aba_9 -0.298000000 -0.83072052 0.234720519
## M248_S_noaba_9-M058_S_1aba_9 -0.266111111 -0.81342942 0.281207193
## M248_C_10aba_9-M058_S_noaba_9 -0.147000000 -0.67972052 0.385720519
## M248_C_1aba_9-M058_S_noaba_9 -0.093285714 -0.68031513 0.493743706
## M248_C_noaba_9-M058_S_noaba_9 0.471000000 -0.06172052 1.003720519
## M248_S_10aba_9-M058_S_noaba_9 -0.034555556 -0.58187386 0.512762749
## M248_S_1aba_9-M058_S_noaba_9 -0.102000000 -0.63472052 0.430720519
## M248_S_noaba_9-M058_S_noaba_9 -0.070111111 -0.61742942 0.477207193
## M248_C_1aba_9-M248_C_10aba_9 0.053714286 -0.53331513 0.640743706
## M248_C_noaba_9-M248_C_10aba_9 0.618000000 0.08527948 1.150720519
## M248_S_10aba_9-M248_C_10aba_9 0.112444444 -0.43487386 0.659762749
## M248_S_1aba_9-M248_C_10aba_9 0.045000000 -0.48772052 0.577720519
## M248_S_noaba_9-M248_C_10aba_9 0.076888889 -0.47042942 0.624207193
## M248_C_noaba_9-M248_C_1aba_9 0.564285714 -0.02274371 1.151315135
## M248_S_10aba_9-M248_C_1aba_9 0.058730159 -0.54157786 0.659038176
## M248_S_1aba_9-M248_C_1aba_9 -0.008714286 -0.59574371 0.578315135
## M248_S_noaba_9-M248_C_1aba_9 0.023174603 -0.57713341 0.623482621
## M248_S_10aba_9-M248_C_noaba_9 -0.505555556 -1.05287386 0.041762749
## M248_S_1aba_9-M248_C_noaba_9 -0.573000000 -1.10572052 -0.040279481
## M248_S_noaba_9-M248_C_noaba_9 -0.541111111 -1.08842942 0.006207193
## M248_S_1aba_9-M248_S_10aba_9 -0.067444444 -0.61476275 0.479873860
## M248_S_noaba_9-M248_S_10aba_9 -0.035555556 -0.59709229 0.525981176
## M248_S_noaba_9-M248_S_1aba_9 0.031888889 -0.51542942 0.579207193
## p adj
## LA1511_C_1aba_9-LA1511_C_10aba_9 0.9999999
## LA1511_C_noaba_9-LA1511_C_10aba_9 1.0000000
## LA1511_S_10aba_9-LA1511_C_10aba_9 0.9999998
## LA1511_S_1aba_9-LA1511_C_10aba_9 0.9999999
## LA1511_S_noaba_9-LA1511_C_10aba_9 0.9999881
## M058_C_10aba_9-LA1511_C_10aba_9 0.9877796
## M058_C_1aba_9-LA1511_C_10aba_9 0.9999998
## M058_C_noaba_9-LA1511_C_10aba_9 0.9947003
## M058_S_10aba_9-LA1511_C_10aba_9 0.9995563
## M058_S_1aba_9-LA1511_C_10aba_9 0.9999751
## M058_S_noaba_9-LA1511_C_10aba_9 1.0000000
## M248_C_10aba_9-LA1511_C_10aba_9 0.9963838
## M248_C_1aba_9-LA1511_C_10aba_9 0.9999810
## M248_C_noaba_9-LA1511_C_10aba_9 0.3495755
## M248_S_10aba_9-LA1511_C_10aba_9 1.0000000
## M248_S_1aba_9-LA1511_C_10aba_9 0.9998403
## M248_S_noaba_9-LA1511_C_10aba_9 0.9999954
## LA1511_C_noaba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_10aba_9-LA1511_C_1aba_9 0.9991113
## LA1511_S_1aba_9-LA1511_C_1aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_1aba_9 1.0000000
## M058_C_10aba_9-LA1511_C_1aba_9 0.9999973
## M058_C_1aba_9-LA1511_C_1aba_9 1.0000000
## M058_C_noaba_9-LA1511_C_1aba_9 0.9999997
## M058_S_10aba_9-LA1511_C_1aba_9 0.9651043
## M058_S_1aba_9-LA1511_C_1aba_9 1.0000000
## M058_S_noaba_9-LA1511_C_1aba_9 0.9999314
## M248_C_10aba_9-LA1511_C_1aba_9 0.8990567
## M248_C_1aba_9-LA1511_C_1aba_9 0.9925709
## M248_C_noaba_9-LA1511_C_1aba_9 0.8805291
## M248_S_10aba_9-LA1511_C_1aba_9 0.9993192
## M248_S_1aba_9-LA1511_C_1aba_9 0.9743383
## M248_S_noaba_9-LA1511_C_1aba_9 0.9948653
## LA1511_S_10aba_9-LA1511_C_noaba_9 0.9999773
## LA1511_S_1aba_9-LA1511_C_noaba_9 1.0000000
## LA1511_S_noaba_9-LA1511_C_noaba_9 1.0000000
## M058_C_10aba_9-LA1511_C_noaba_9 0.9993030
## M058_C_1aba_9-LA1511_C_noaba_9 1.0000000
## M058_C_noaba_9-LA1511_C_noaba_9 0.9998038
## M058_S_10aba_9-LA1511_C_noaba_9 0.9951717
## M058_S_1aba_9-LA1511_C_noaba_9 1.0000000
## M058_S_noaba_9-LA1511_C_noaba_9 0.9999998
## M248_C_10aba_9-LA1511_C_noaba_9 0.9773251
## M248_C_1aba_9-LA1511_C_noaba_9 0.9995011
## M248_C_noaba_9-LA1511_C_noaba_9 0.6130149
## M248_S_10aba_9-LA1511_C_noaba_9 0.9999909
## M248_S_1aba_9-LA1511_C_noaba_9 0.9973412
## M248_S_noaba_9-LA1511_C_noaba_9 0.9997704
## LA1511_S_1aba_9-LA1511_S_10aba_9 0.9988695
## LA1511_S_noaba_9-LA1511_S_10aba_9 0.9930582
## M058_C_10aba_9-LA1511_S_10aba_9 0.8660562
## M058_C_1aba_9-LA1511_S_10aba_9 0.9989509
## M058_C_noaba_9-LA1511_S_10aba_9 0.9078254
## M058_S_10aba_9-LA1511_S_10aba_9 1.0000000
## M058_S_1aba_9-LA1511_S_10aba_9 0.9906450
## M058_S_noaba_9-LA1511_S_10aba_9 1.0000000
## M248_C_10aba_9-LA1511_S_10aba_9 1.0000000
## M248_C_1aba_9-LA1511_S_10aba_9 1.0000000
## M248_C_noaba_9-LA1511_S_10aba_9 0.1822949
## M248_S_10aba_9-LA1511_S_10aba_9 1.0000000
## M248_S_1aba_9-LA1511_S_10aba_9 1.0000000
## M248_S_noaba_9-LA1511_S_10aba_9 1.0000000
## LA1511_S_noaba_9-LA1511_S_1aba_9 1.0000000
## M058_C_10aba_9-LA1511_S_1aba_9 0.9999881
## M058_C_1aba_9-LA1511_S_1aba_9 1.0000000
## M058_C_noaba_9-LA1511_S_1aba_9 0.9999985
## M058_S_10aba_9-LA1511_S_1aba_9 0.9530290
## M058_S_1aba_9-LA1511_S_1aba_9 1.0000000
## M058_S_noaba_9-LA1511_S_1aba_9 0.9999052
## M248_C_10aba_9-LA1511_S_1aba_9 0.8640085
## M248_C_1aba_9-LA1511_S_1aba_9 0.9900847
## M248_C_noaba_9-LA1511_S_1aba_9 0.7996130
## M248_S_10aba_9-LA1511_S_1aba_9 0.9990440
## M248_S_1aba_9-LA1511_S_1aba_9 0.9635575
## M248_S_noaba_9-LA1511_S_1aba_9 0.9927208
## M058_C_10aba_9-LA1511_S_noaba_9 0.9999999
## M058_C_1aba_9-LA1511_S_noaba_9 1.0000000
## M058_C_noaba_9-LA1511_S_noaba_9 1.0000000
## M058_S_10aba_9-LA1511_S_noaba_9 0.8755920
## M058_S_1aba_9-LA1511_S_noaba_9 1.0000000
## M058_S_noaba_9-LA1511_S_noaba_9 0.9985349
## M248_C_10aba_9-LA1511_S_noaba_9 0.7230414
## M248_C_1aba_9-LA1511_S_noaba_9 0.9620088
## M248_C_noaba_9-LA1511_S_noaba_9 0.9142749
## M248_S_10aba_9-LA1511_S_noaba_9 0.9925616
## M248_S_1aba_9-LA1511_S_noaba_9 0.8909557
## M248_S_noaba_9-LA1511_S_noaba_9 0.9670714
## M058_C_1aba_9-M058_C_10aba_9 0.9999995
## M058_C_noaba_9-M058_C_10aba_9 1.0000000
## M058_S_10aba_9-M058_C_10aba_9 0.4754737
## M058_S_1aba_9-M058_C_10aba_9 1.0000000
## M058_S_noaba_9-M058_C_10aba_9 0.9069039
## M248_C_10aba_9-M058_C_10aba_9 0.2766108
## M248_C_1aba_9-M058_C_10aba_9 0.6893433
## M248_C_noaba_9-M058_C_10aba_9 0.9987952
## M248_S_10aba_9-M058_C_10aba_9 0.8261316
## M248_S_1aba_9-M058_C_10aba_9 0.4744377
## M248_S_noaba_9-M058_C_10aba_9 0.6782175
## M058_C_noaba_9-M058_C_1aba_9 1.0000000
## M058_S_10aba_9-M058_C_1aba_9 0.9654478
## M058_S_1aba_9-M058_C_1aba_9 1.0000000
## M058_S_noaba_9-M058_C_1aba_9 0.9999086
## M248_C_10aba_9-M058_C_1aba_9 0.9043900
## M248_C_1aba_9-M058_C_1aba_9 0.9921305
## M248_C_noaba_9-M058_C_1aba_9 0.9302718
## M248_S_10aba_9-M058_C_1aba_9 0.9992052
## M248_S_1aba_9-M058_C_1aba_9 0.9747858
## M248_S_noaba_9-M058_C_1aba_9 0.9945787
## M058_S_10aba_9-M058_C_noaba_9 0.5547597
## M058_S_1aba_9-M058_C_noaba_9 1.0000000
## M058_S_noaba_9-M058_C_noaba_9 0.9435055
## M248_C_10aba_9-M058_C_noaba_9 0.3452753
## M248_C_1aba_9-M058_C_noaba_9 0.7589740
## M248_C_noaba_9-M058_C_noaba_9 0.9965827
## M248_S_10aba_9-M058_C_noaba_9 0.8809480
## M248_S_1aba_9-M058_C_noaba_9 0.5585488
## M248_S_noaba_9-M058_C_noaba_9 0.7536647
## M058_S_1aba_9-M058_S_10aba_9 0.8546349
## M058_S_noaba_9-M058_S_10aba_9 0.9999977
## M248_C_10aba_9-M058_S_10aba_9 1.0000000
## M248_C_1aba_9-M058_S_10aba_9 1.0000000
## M248_C_noaba_9-M058_S_10aba_9 0.0271336
## M248_S_10aba_9-M058_S_10aba_9 1.0000000
## M248_S_1aba_9-M058_S_10aba_9 1.0000000
## M248_S_noaba_9-M058_S_10aba_9 1.0000000
## M058_S_noaba_9-M058_S_1aba_9 0.9977328
## M248_C_10aba_9-M058_S_1aba_9 0.6907015
## M248_C_1aba_9-M058_S_1aba_9 0.9527363
## M248_C_noaba_9-M058_S_1aba_9 0.9299352
## M248_S_10aba_9-M058_S_1aba_9 0.9896516
## M248_S_1aba_9-M058_S_1aba_9 0.8703089
## M248_S_noaba_9-M058_S_1aba_9 0.9580419
## M248_C_10aba_9-M058_S_noaba_9 0.9999454
## M248_C_1aba_9-M058_S_noaba_9 1.0000000
## M248_C_noaba_9-M058_S_noaba_9 0.1539659
## M248_S_10aba_9-M058_S_noaba_9 1.0000000
## M248_S_1aba_9-M058_S_noaba_9 0.9999998
## M248_S_noaba_9-M058_S_noaba_9 1.0000000
## M248_C_1aba_9-M248_C_10aba_9 1.0000000
## M248_C_noaba_9-M248_C_10aba_9 0.0075806
## M248_S_10aba_9-M248_C_10aba_9 0.9999993
## M248_S_1aba_9-M248_C_10aba_9 1.0000000
## M248_S_noaba_9-M248_C_10aba_9 1.0000000
## M248_C_noaba_9-M248_C_1aba_9 0.0746654
## M248_S_10aba_9-M248_C_1aba_9 1.0000000
## M248_S_1aba_9-M248_C_1aba_9 1.0000000
## M248_S_noaba_9-M248_C_1aba_9 1.0000000
## M248_S_10aba_9-M248_C_noaba_9 0.1075976
## M248_S_1aba_9-M248_C_noaba_9 0.0214214
## M248_S_noaba_9-M248_C_noaba_9 0.0563651
## M248_S_1aba_9-M248_S_10aba_9 1.0000000
## M248_S_noaba_9-M248_S_10aba_9 1.0000000
## M248_S_noaba_9-M248_S_1aba_9 1.0000000
P8 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P8)
stat.test
## LA1511_C_1aba_9 LA1511_C_noaba_9 LA1511_S_10aba_9 LA1511_S_1aba_9
## "ab" "ab" "ab" "ab"
## LA1511_S_noaba_9 M058_C_10aba_9 M058_C_1aba_9 M058_C_noaba_9
## "ab" "ab" "ab" "ab"
## M058_S_10aba_9 M058_S_1aba_9 M058_S_noaba_9 M248_C_10aba_9
## "a" "ab" "ab" "a"
## M248_C_1aba_9 M248_C_noaba_9 M248_S_10aba_9 M248_S_1aba_9
## "ab" "b" "ab" "a"
## M248_S_noaba_9 LA1511_C_10aba_9
## "ab" "ab"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ABA_pareto_location$Condition.all <- factor(ABA_pareto_location$Condition.all, levels = c("C_noaba", "C_1aba","C_10aba", "S_noaba","S_1aba","S_10aba"))
ABA_pareto_location_nonscale <- ggplot(data = ABA_pareto_location, mapping = aes(x = All.ID, y = pareto.front.nonscaling.location
, colour = Condition.all))
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + ylab("Pareto front nonscaling location") + xlab("") #+ #ggtitle("")
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + stat_pvalue_manual(test, label = "Tukey", y.position = 1.5)
ABA_pareto_location_nonscale
ABA_pareto_location_nonscale <- ggplot(data=ABA_pareto_location, aes(x= Condition.all, y=pareto.front.nonscaling.location, color = Condition.all))
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + facet_grid(~ Accessions )
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_location_nonscale <- ABA_pareto_location_nonscale + ylab("Pareto front nonscaling location") + xlab("") + theme(legend.position='none') + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
ABA_pareto_location_nonscale
aov(pareto.front.nonscaling.distance ~ All.ID, data = ABA_pareto_location)
## Call:
## aov(formula = pareto.front.nonscaling.distance ~ All.ID, data = ABA_pareto_location)
##
## Terms:
## All.ID Residuals
## Sum of Squares 672.6592 587.8346
## Deg. of Freedom 17 145
##
## Residual standard error: 2.013463
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.nonscaling.distance ~ All.ID, data = ABA_pareto_location))
Output
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = pareto.front.nonscaling.distance ~ All.ID, data = ABA_pareto_location)
##
## $All.ID
## diff lwr upr p adj
## LA1511_C_1aba_9-LA1511_C_10aba_9 0.2164239 -3.1767704715 3.6096182 1.0000000
## LA1511_C_noaba_9-LA1511_C_10aba_9 2.0815979 -1.2052001116 5.3683960 0.7167479
## LA1511_S_10aba_9-LA1511_C_10aba_9 -2.7839930 -6.4780351098 0.9100491 0.4055622
## LA1511_S_1aba_9-LA1511_C_10aba_9 -1.5695456 -4.7686799098 1.6295887 0.9545437
## LA1511_S_noaba_9-LA1511_C_10aba_9 -1.8707403 -5.0698746098 1.3283940 0.8243540
## M058_C_10aba_9-LA1511_C_10aba_9 -2.0195245 -5.2186588098 1.1796098 0.7217185
## M058_C_1aba_9-LA1511_C_10aba_9 1.1045531 -2.4207212405 4.6298274 0.9996957
## M058_C_noaba_9-LA1511_C_10aba_9 0.5009115 -2.6982228098 3.7000458 1.0000000
## M058_S_10aba_9-LA1511_C_10aba_9 -2.2854770 -5.6786713465 1.1077173 0.6141893
## M058_S_1aba_9-LA1511_C_10aba_9 -0.8423000 -4.0414343098 2.3568343 0.9999717
## M058_S_noaba_9-LA1511_C_10aba_9 -1.6076117 -4.8067460098 1.5915226 0.9440422
## M248_C_10aba_9-LA1511_C_10aba_9 1.5922929 -1.6068414098 4.7914272 0.9484577
## M248_C_1aba_9-LA1511_C_10aba_9 3.5547721 0.0294977595 7.0800464 0.0457114
## M248_C_noaba_9-LA1511_C_10aba_9 5.1450246 1.9458902902 8.3441589 0.0000089
## M248_S_10aba_9-LA1511_C_10aba_9 -1.0942264 -4.3810244450 2.1925717 0.9993350
## M248_S_1aba_9-LA1511_C_10aba_9 -0.6668041 -3.8659384098 2.5323302 0.9999991
## M248_S_noaba_9-LA1511_C_10aba_9 0.8752059 -2.4115921116 4.1620040 0.9999668
## LA1511_C_noaba_9-LA1511_C_1aba_9 1.8651741 -1.6107932784 5.3411414 0.9047344
## LA1511_S_10aba_9-LA1511_C_1aba_9 -3.0004169 -6.8637385870 0.8629048 0.3507282
## LA1511_S_1aba_9-LA1511_C_1aba_9 -1.7859695 -5.1791638215 1.6072249 0.9180630
## LA1511_S_noaba_9-LA1511_C_1aba_9 -2.0871642 -5.4803585215 1.3060302 0.7597604
## M058_C_10aba_9-LA1511_C_1aba_9 -2.2359484 -5.6291427215 1.1572460 0.6522883
## M058_C_1aba_9-LA1511_C_1aba_9 0.8881292 -2.8141493609 4.5904078 0.9999926
## M058_C_noaba_9-LA1511_C_1aba_9 0.2844876 -3.1087067215 3.6776820 1.0000000
## M058_S_10aba_9-LA1511_C_1aba_9 -2.5019009 -6.0786417679 1.0748400 0.5454159
## M058_S_1aba_9-LA1511_C_1aba_9 -1.0587239 -4.4519182215 2.3344705 0.9997120
## M058_S_noaba_9-LA1511_C_1aba_9 -1.8240356 -5.2172299215 1.5691588 0.9034105
## M248_C_10aba_9-LA1511_C_1aba_9 1.3758690 -2.0173253215 4.7690634 0.9931318
## M248_C_1aba_9-LA1511_C_1aba_9 3.3383482 -0.3639303609 7.0406268 0.1317763
## M248_C_noaba_9-LA1511_C_1aba_9 4.9286007 1.5354063785 8.3217951 0.0001136
## M248_S_10aba_9-LA1511_C_1aba_9 -1.3106503 -4.7866176117 2.1653171 0.9969761
## M248_S_1aba_9-LA1511_C_1aba_9 -0.8832280 -4.2764223215 2.5099664 0.9999760
## M248_S_noaba_9-LA1511_C_1aba_9 0.6587821 -2.8171852784 4.1347494 0.9999998
## LA1511_S_10aba_9-LA1511_C_noaba_9 -4.8655909 -8.6358068850 -1.0953750 0.0012922
## LA1511_S_1aba_9-LA1511_C_noaba_9 -3.6511435 -6.9379416005 -0.3643455 0.0140433
## LA1511_S_noaba_9-LA1511_C_noaba_9 -3.9523382 -7.2391363005 -0.6655402 0.0043541
## M058_C_10aba_9-LA1511_C_noaba_9 -4.1011224 -7.3879205005 -0.8143244 0.0023557
## M058_C_1aba_9-LA1511_C_noaba_9 -0.9770449 -4.5820608375 2.6279711 0.9999575
## M058_C_noaba_9-LA1511_C_noaba_9 -1.5806864 -4.8674845005 1.7061116 0.9619741
## M058_S_10aba_9-LA1511_C_noaba_9 -4.3670749 -7.8430422922 -0.8911076 0.0020908
## M058_S_1aba_9-LA1511_C_noaba_9 -2.9238979 -6.2106960005 0.3629001 0.1467972
## M058_S_noaba_9-LA1511_C_noaba_9 -3.6892096 -6.9760077005 -0.4024116 0.0121805
## M248_C_10aba_9-LA1511_C_noaba_9 -0.4893050 -3.7761031005 2.7974930 1.0000000
## M248_C_1aba_9-LA1511_C_noaba_9 1.4731741 -2.1318418375 5.0781901 0.9925240
## M248_C_noaba_9-LA1511_C_noaba_9 3.0634267 -0.2233714005 6.3502247 0.0994136
## M248_S_10aba_9-LA1511_C_noaba_9 -3.1758243 -6.5480079865 0.1963593 0.0905161
## M248_S_1aba_9-LA1511_C_noaba_9 -2.7484020 -6.0352001005 0.5383960 0.2286700
## M248_S_noaba_9-LA1511_C_noaba_9 -1.2063920 -4.5785756532 2.1657917 0.9983793
## LA1511_S_1aba_9-LA1511_S_10aba_9 1.2144474 -2.4795947098 4.9084895 0.9994332
## LA1511_S_noaba_9-LA1511_S_10aba_9 0.9132527 -2.7807894098 4.6072948 0.9999885
## M058_C_10aba_9-LA1511_S_10aba_9 0.7644685 -2.9295736098 4.4585106 0.9999992
## M058_C_1aba_9-LA1511_S_10aba_9 3.8885461 -0.0912837932 7.8683759 0.0635793
## M058_C_noaba_9-LA1511_S_10aba_9 3.2849045 -0.4091376098 6.9789466 0.1472430
## M058_S_10aba_9-LA1511_S_10aba_9 0.4985160 -3.3648057120 4.3618377 1.0000000
## M058_S_1aba_9-LA1511_S_10aba_9 1.9416930 -1.7523491098 5.6357351 0.9189377
## M058_S_noaba_9-LA1511_S_10aba_9 1.1763813 -2.5176608098 4.8704234 0.9996239
## M248_C_10aba_9-LA1511_S_10aba_9 4.3762859 0.6822437902 8.0703280 0.0055092
## M248_C_1aba_9-LA1511_S_10aba_9 6.3387651 2.3589352068 10.3185949 0.0000116
## M248_C_noaba_9-LA1511_S_10aba_9 7.9290176 4.2349754902 11.6230597 0.0000000
## M248_S_10aba_9-LA1511_S_10aba_9 1.6897666 -2.0804493295 5.4599826 0.9805013
## M248_S_1aba_9-LA1511_S_10aba_9 2.1171889 -1.5768532098 5.8112310 0.8463901
## M248_S_noaba_9-LA1511_S_10aba_9 3.6591989 -0.1110169962 7.4294149 0.0679629
## LA1511_S_noaba_9-LA1511_S_1aba_9 -0.3011947 -3.5003290098 2.8979396 1.0000000
## M058_C_10aba_9-LA1511_S_1aba_9 -0.4499789 -3.6491132098 2.7491554 1.0000000
## M058_C_1aba_9-LA1511_S_1aba_9 2.6740987 -0.8511756405 6.1993730 0.3935628
## M058_C_noaba_9-LA1511_S_1aba_9 2.0704571 -1.1286772098 5.2695914 0.6823325
## M058_S_10aba_9-LA1511_S_1aba_9 -0.7159314 -4.1091257465 2.6772629 0.9999989
## M058_S_1aba_9-LA1511_S_1aba_9 0.7272456 -2.4718887098 3.9263799 0.9999966
## M058_S_noaba_9-LA1511_S_1aba_9 -0.0380661 -3.2372004098 3.1610682 1.0000000
## M248_C_10aba_9-LA1511_S_1aba_9 3.1618385 -0.0372958098 6.3609728 0.0565525
## M248_C_1aba_9-LA1511_S_1aba_9 5.1243177 1.5990433595 8.6495920 0.0001116
## M248_C_noaba_9-LA1511_S_1aba_9 6.7145702 3.5154358902 9.9137045 0.0000000
## M248_S_10aba_9-LA1511_S_1aba_9 0.4753192 -2.8114788450 3.7621173 1.0000000
## M248_S_1aba_9-LA1511_S_1aba_9 0.9027415 -2.2963928098 4.1018758 0.9999256
## M248_S_noaba_9-LA1511_S_1aba_9 2.4447515 -0.8420465116 5.7315496 0.4300473
## M058_C_10aba_9-LA1511_S_noaba_9 -0.1487842 -3.3479185098 3.0503501 1.0000000
## M058_C_1aba_9-LA1511_S_noaba_9 2.9752934 -0.5499809405 6.5005677 0.2150748
## M058_C_noaba_9-LA1511_S_noaba_9 2.3716518 -0.8274825098 5.5707861 0.4362748
## M058_S_10aba_9-LA1511_S_noaba_9 -0.4147367 -3.8079310465 2.9784576 1.0000000
## M058_S_1aba_9-LA1511_S_noaba_9 1.0284403 -2.1706940098 4.2275746 0.9995749
## M058_S_noaba_9-LA1511_S_noaba_9 0.2631286 -2.9360057098 3.4622629 1.0000000
## M248_C_10aba_9-LA1511_S_noaba_9 3.4630332 0.2638988902 6.6621675 0.0197521
## M248_C_1aba_9-LA1511_S_noaba_9 5.4255124 1.9002380595 8.9507867 0.0000283
## M248_C_noaba_9-LA1511_S_noaba_9 7.0157649 3.8166305902 10.2148992 0.0000000
## M248_S_10aba_9-LA1511_S_noaba_9 0.7765139 -2.5102841450 4.0633120 0.9999941
## M248_S_1aba_9-LA1511_S_noaba_9 1.2039362 -1.9951981098 4.4030705 0.9970434
## M248_S_noaba_9-LA1511_S_noaba_9 2.7459462 -0.5408518116 6.0327443 0.2300030
## M058_C_1aba_9-M058_C_10aba_9 3.1240776 -0.4011967405 6.6493519 0.1512334
## M058_C_noaba_9-M058_C_10aba_9 2.5204360 -0.6786983098 5.7195703 0.3254224
## M058_S_10aba_9-M058_C_10aba_9 -0.2659525 -3.6591468465 3.1272418 1.0000000
## M058_S_1aba_9-M058_C_10aba_9 1.1772245 -2.0219098098 4.3763588 0.9977284
## M058_S_noaba_9-M058_C_10aba_9 0.4119128 -2.7872215098 3.6110471 1.0000000
## M248_C_10aba_9-M058_C_10aba_9 3.6118174 0.4126830902 6.8109517 0.0112279
## M248_C_1aba_9-M058_C_10aba_9 5.5742966 2.0490222595 9.0995709 0.0000141
## M248_C_noaba_9-M058_C_10aba_9 7.1645491 3.9654147902 10.3636834 0.0000000
## M248_S_10aba_9-M058_C_10aba_9 0.9252981 -2.3614999450 4.2120962 0.9999279
## M248_S_1aba_9-M058_C_10aba_9 1.3527204 -1.8464139098 4.5518547 0.9892319
## M248_S_noaba_9-M058_C_10aba_9 2.8947304 -0.3920676116 6.1815285 0.1586088
## M058_C_noaba_9-M058_C_1aba_9 -0.6036416 -4.1289158834 2.9216327 1.0000000
## M058_S_10aba_9-M058_C_1aba_9 -3.3900301 -7.0923086287 0.3122485 0.1159825
## M058_S_1aba_9-M058_C_1aba_9 -1.9468531 -5.4721273834 1.5784212 0.8817953
## M058_S_noaba_9-M058_C_1aba_9 -2.7121648 -6.2374390834 0.8131095 0.3677155
## M248_C_10aba_9-M058_C_1aba_9 0.4877398 -3.0375344834 4.0130141 1.0000000
## M248_C_1aba_9-M058_C_1aba_9 2.4502190 -1.3734778521 6.2739159 0.6983525
## M248_C_noaba_9-M058_C_1aba_9 4.0404715 0.5151972166 7.5657458 0.0090540
## M248_S_10aba_9-M058_C_1aba_9 -2.1987795 -5.8037954248 1.4062365 0.7714595
## M248_S_1aba_9-M058_C_1aba_9 -1.7713572 -5.2966314834 1.7539171 0.9440812
## M248_S_noaba_9-M058_C_1aba_9 -0.2293471 -3.8343630914 3.3756688 1.0000000
## M058_S_10aba_9-M058_C_noaba_9 -2.7863885 -6.1795828465 0.6068058 0.2564735
## M058_S_1aba_9-M058_C_noaba_9 -1.3432115 -4.5423458098 1.8559228 0.9900040
## M058_S_noaba_9-M058_C_noaba_9 -2.1085232 -5.3076575098 1.0906111 0.6519242
## M248_C_10aba_9-M058_C_noaba_9 1.0913814 -2.1077529098 4.2905157 0.9990959
## M248_C_1aba_9-M058_C_noaba_9 3.0538606 -0.4714137405 6.5791349 0.1793301
## M248_C_noaba_9-M058_C_noaba_9 4.6441131 1.4449787902 7.8432474 0.0001150
## M248_S_10aba_9-M058_C_noaba_9 -1.5951379 -4.8819359450 1.6916602 0.9587255
## M248_S_1aba_9-M058_C_noaba_9 -1.1677156 -4.3668499098 2.0314187 0.9979371
## M248_S_noaba_9-M058_C_noaba_9 0.3742944 -2.9125036116 3.6610925 1.0000000
## M058_S_1aba_9-M058_S_10aba_9 1.4431770 -1.9500173465 4.8363713 0.9885525
## M058_S_noaba_9-M058_S_10aba_9 0.6778653 -2.7153290465 4.0710596 0.9999995
## M248_C_10aba_9-M058_S_10aba_9 3.8777699 0.4845755535 7.2709642 0.0094438
## M248_C_1aba_9-M058_S_10aba_9 5.8402491 2.1379705141 9.5425276 0.0000150
## M248_C_noaba_9-M058_S_10aba_9 7.4305016 4.0373072535 10.8236959 0.0000000
## M248_S_10aba_9-M058_S_10aba_9 1.1912506 -2.2847167367 4.6672180 0.9990430
## M248_S_1aba_9-M058_S_10aba_9 1.6186729 -1.7745214465 5.0118672 0.9646827
## M248_S_noaba_9-M058_S_10aba_9 3.1606829 -0.3152844034 6.6366503 0.1229865
## M058_S_noaba_9-M058_S_1aba_9 -0.7653117 -3.9644460098 2.4338226 0.9999929
## M248_C_10aba_9-M058_S_1aba_9 2.4345929 -0.7645414098 5.6337272 0.3875911
## M248_C_1aba_9-M058_S_1aba_9 4.3970721 0.8717977595 7.9223464 0.0023706
## M248_C_noaba_9-M058_S_1aba_9 5.9873246 2.7881902902 9.1864589 0.0000001
## M248_S_10aba_9-M058_S_1aba_9 -0.2519264 -3.5387244450 3.0348717 1.0000000
## M248_S_1aba_9-M058_S_1aba_9 0.1754959 -3.0236384098 3.3746302 1.0000000
## M248_S_noaba_9-M058_S_1aba_9 1.7175059 -1.5692921116 5.0043040 0.9226590
## M248_C_10aba_9-M058_S_noaba_9 3.1999046 0.0007702902 6.3990389 0.0498719
## M248_C_1aba_9-M058_S_noaba_9 5.1623838 1.6371094595 8.6876581 0.0000941
## M248_C_noaba_9-M058_S_noaba_9 6.7526363 3.5535019902 9.9517706 0.0000000
## M248_S_10aba_9-M058_S_noaba_9 0.5133853 -2.7734127450 3.8001834 1.0000000
## M248_S_1aba_9-M058_S_noaba_9 0.9408076 -2.2583267098 4.1399419 0.9998692
## M248_S_noaba_9-M058_S_noaba_9 2.4828176 -0.8039804116 5.7696157 0.4012726
## M248_C_1aba_9-M248_C_10aba_9 1.9624792 -1.5627951405 5.4877535 0.8747373
## M248_C_noaba_9-M248_C_10aba_9 3.5527317 0.3535973902 6.7518660 0.0140987
## M248_S_10aba_9-M248_C_10aba_9 -2.6865193 -5.9733173450 0.6002788 0.2638422
## M248_S_1aba_9-M248_C_10aba_9 -2.2590970 -5.4582313098 0.9400373 0.5277346
## M248_S_noaba_9-M248_C_10aba_9 -0.7170870 -4.0038850116 2.5697111 0.9999982
## M248_C_noaba_9-M248_C_1aba_9 1.5902525 -1.9350217834 5.1155268 0.9792178
## M248_S_10aba_9-M248_C_1aba_9 -4.6489985 -8.2540144248 -1.0439825 0.0013096
## M248_S_1aba_9-M248_C_1aba_9 -4.2215762 -7.7468504834 -0.6963019 0.0046516
## M248_S_noaba_9-M248_C_1aba_9 -2.6795661 -6.2845820914 0.9254498 0.4313599
## M248_S_10aba_9-M248_C_noaba_9 -6.2392510 -9.5260490450 -2.9524529 0.0000001
## M248_S_1aba_9-M248_C_noaba_9 -5.8118287 -9.0109630098 -2.6126944 0.0000002
## M248_S_noaba_9-M248_C_noaba_9 -4.2698187 -7.5566167116 -0.9830206 0.0011435
## M248_S_1aba_9-M248_S_10aba_9 0.4274223 -2.8593757672 3.7142203 1.0000000
## M248_S_noaba_9-M248_S_10aba_9 1.9694323 -1.4027513199 5.3416160 0.8258072
## M248_S_noaba_9-M248_S_1aba_9 1.5420100 -1.7447880116 4.8288081 0.9697312
P7 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P7)
stat.test
## LA1511_C_1aba_9 LA1511_C_noaba_9 LA1511_S_10aba_9 LA1511_S_1aba_9
## "abcd" "ace" "b" "bd"
## LA1511_S_noaba_9 M058_C_10aba_9 M058_C_1aba_9 M058_C_noaba_9
## "b" "b" "abcd" "abcd"
## M058_S_10aba_9 M058_S_1aba_9 M058_S_noaba_9 M248_C_10aba_9
## "b" "abd" "b" "acd"
## M248_C_1aba_9 M248_C_noaba_9 M248_S_10aba_9 M248_S_1aba_9
## "ce" "e" "abd" "abd"
## M248_S_noaba_9 LA1511_C_10aba_9
## "abcd" "abd"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ABA_pareto_location$Condition.all <- factor(ABA_pareto_location$Condition.all, levels = c("C_noaba", "C_1aba","C_10aba", "S_noaba","S_1aba","S_10aba"))
ABA_pareto_distance_nonscale <- ggplot(data = ABA_pareto_location, mapping = aes(x = All.ID, y = pareto.front.nonscaling.distance, colour = Condition.all))
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + ylab("Pareto front nonscaling distance") + xlab("") #+ #ggtitle("")
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + stat_pvalue_manual(test, label = "Tukey", y.position = 15)
ABA_pareto_distance_nonscale
ABA_pareto_distance_nonscale <- ggplot(data=ABA_pareto_location, aes(x= Condition.all, y=pareto.front.nonscaling.distance, color = Condition.all))
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + facet_grid(~ Accessions )
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ABA_pareto_distance_nonscale <- ABA_pareto_distance_nonscale + ylab("Pareto front nonscaling distance") + xlab("") + theme(legend.position='none') + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
ABA_pareto_distance_nonscale
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