This is a pareto-front components calculation for 3 tomatoes experienced GA3 and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220315_RSA_M248M058LA1511_GA_100mM_Salt-selected. The root tracing was done by Stacey Na in March 2023.

getwd()
## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20230509_GA_pareto-front_components"
list.files(pattern = ".csv")
## [1] "GA-Pareto-scaling-nonscaling-analysis.csv"
GA_pareto_location <-read.csv("GA-Pareto-scaling-nonscaling-analysis.csv")
GA_pareto_location
GA_pareto_location$Condition.all <- paste(GA_pareto_location$Condition, GA_pareto_location$Condition2, sep="_")
GA_pareto_location
library(ggplot2)
library(ggpubr)
library(multcompView)
GA_pareto_location$Accessions <- gsub("la1511", "LA1511", GA_pareto_location$Accessions)

GA_pareto_location$All.ID <- paste(GA_pareto_location$Accessions, GA_pareto_location$Condition.all, GA_pareto_location$Day, sep="_")
GA_pareto_location
GA_pareto_location2 <- subset(GA_pareto_location, GA_pareto_location$Day > 5)
GA_pareto_location2
aov(pareto.front.scaling.location ~ All.ID, data = GA_pareto_location2)
## Call:
##    aov(formula = pareto.front.scaling.location ~ All.ID, data = GA_pareto_location2)
## 
## Terms:
##                    All.ID Residuals
## Sum of Squares   2.235256 13.705441
## Deg. of Freedom        17       163
## 
## Residual standard error: 0.2899698
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.scaling.location ~ All.ID, data = GA_pareto_location2))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = pareto.front.scaling.location ~ All.ID, data = GA_pareto_location2)
## 
## $All.ID
##                                          diff         lwr        upr     p adj
## LA1511_C_loga_9-LA1511_C_higa_9  0.0908181818 -0.35841314 0.54004951 0.9999995
## LA1511_C_noga_9-LA1511_C_higa_9 -0.0401818182 -0.48941314 0.40904951 1.0000000
## LA1511_S_higa_9-LA1511_C_higa_9 -0.0400000000 -0.47840488 0.39840488 1.0000000
## LA1511_S_loga_9-LA1511_C_higa_9 -0.0900000000 -0.52840488 0.34840488 0.9999993
## LA1511_S_noga_9-LA1511_C_higa_9 -0.0115151515 -0.47363447 0.45060417 1.0000000
## M058_C_higa_9-LA1511_C_higa_9    0.1258181818 -0.32341314 0.57504951 0.9999366
## M058_C_loga_9-LA1511_C_higa_9    0.0008181818 -0.44841314 0.45004951 1.0000000
## M058_C_noga_9-LA1511_C_higa_9    0.1688181818 -0.28041314 0.61804951 0.9972134
## M058_S_higa_9-LA1511_C_higa_9    0.2078181818 -0.24141314 0.65704951 0.9742834
## M058_S_loga_9-LA1511_C_higa_9    0.2218181818 -0.22741314 0.67104951 0.9531631
## M058_S_noga_9-LA1511_C_higa_9    0.3218181818 -0.14030114 0.78393750 0.5570069
## M248_C_higa_9-LA1511_C_higa_9    0.0688181818 -0.38041314 0.51804951 1.0000000
## M248_C_loga_9-LA1511_C_higa_9    0.0388181818 -0.41041314 0.48804951 1.0000000
## M248_C_noga_9-LA1511_C_higa_9    0.0308181818 -0.41841314 0.48004951 1.0000000
## M248_S_higa_9-LA1511_C_higa_9   -0.0101818182 -0.45941314 0.43904951 1.0000000
## M248_S_loga_9-LA1511_C_higa_9   -0.1041818182 -0.55341314 0.34504951 0.9999958
## M248_S_noga_9-LA1511_C_higa_9   -0.0251818182 -0.47441314 0.42404951 1.0000000
## LA1511_C_noga_9-LA1511_C_loga_9 -0.1310000000 -0.59080292 0.32880292 0.9999197
## LA1511_S_higa_9-LA1511_C_loga_9 -0.1308181818 -0.58004951 0.31841314 0.9998916
## LA1511_S_loga_9-LA1511_C_loga_9 -0.1808181818 -0.63004951 0.26841314 0.9939051
## LA1511_S_noga_9-LA1511_C_loga_9 -0.1023333333 -0.57473593 0.37006926 0.9999985
## M058_C_higa_9-LA1511_C_loga_9    0.0350000000 -0.42480292 0.49480292 1.0000000
## M058_C_loga_9-LA1511_C_loga_9   -0.0900000000 -0.54980292 0.36980292 0.9999997
## M058_C_noga_9-LA1511_C_loga_9    0.0780000000 -0.38180292 0.53780292 1.0000000
## M058_S_higa_9-LA1511_C_loga_9    0.1170000000 -0.34280292 0.57680292 0.9999836
## M058_S_loga_9-LA1511_C_loga_9    0.1310000000 -0.32880292 0.59080292 0.9999197
## M058_S_noga_9-LA1511_C_loga_9    0.2310000000 -0.24140259 0.70340259 0.9570345
## M248_C_higa_9-LA1511_C_loga_9   -0.0220000000 -0.48180292 0.43780292 1.0000000
## M248_C_loga_9-LA1511_C_loga_9   -0.0520000000 -0.51180292 0.40780292 1.0000000
## M248_C_noga_9-LA1511_C_loga_9   -0.0600000000 -0.51980292 0.39980292 1.0000000
## M248_S_higa_9-LA1511_C_loga_9   -0.1010000000 -0.56080292 0.35880292 0.9999981
## M248_S_loga_9-LA1511_C_loga_9   -0.1950000000 -0.65480292 0.26480292 0.9892805
## M248_S_noga_9-LA1511_C_loga_9   -0.1160000000 -0.57580292 0.34380292 0.9999855
## LA1511_S_higa_9-LA1511_C_noga_9  0.0001818182 -0.44904951 0.44941314 1.0000000
## LA1511_S_loga_9-LA1511_C_noga_9 -0.0498181818 -0.49904951 0.39941314 1.0000000
## LA1511_S_noga_9-LA1511_C_noga_9  0.0286666667 -0.44373593 0.50106926 1.0000000
## M058_C_higa_9-LA1511_C_noga_9    0.1660000000 -0.29380292 0.62580292 0.9982701
## M058_C_loga_9-LA1511_C_noga_9    0.0410000000 -0.41880292 0.50080292 1.0000000
## M058_C_noga_9-LA1511_C_noga_9    0.2090000000 -0.25080292 0.66880292 0.9783102
## M058_S_higa_9-LA1511_C_noga_9    0.2480000000 -0.21180292 0.70780292 0.9029675
## M058_S_loga_9-LA1511_C_noga_9    0.2620000000 -0.19780292 0.72180292 0.8549976
## M058_S_noga_9-LA1511_C_noga_9    0.3620000000 -0.11040259 0.83440259 0.3774996
## M248_C_higa_9-LA1511_C_noga_9    0.1090000000 -0.35080292 0.56880292 0.9999942
## M248_C_loga_9-LA1511_C_noga_9    0.0790000000 -0.38080292 0.53880292 1.0000000
## M248_C_noga_9-LA1511_C_noga_9    0.0710000000 -0.38880292 0.53080292 1.0000000
## M248_S_higa_9-LA1511_C_noga_9    0.0300000000 -0.42980292 0.48980292 1.0000000
## M248_S_loga_9-LA1511_C_noga_9   -0.0640000000 -0.52380292 0.39580292 1.0000000
## M248_S_noga_9-LA1511_C_noga_9    0.0150000000 -0.44480292 0.47480292 1.0000000
## LA1511_S_loga_9-LA1511_S_higa_9 -0.0500000000 -0.48840488 0.38840488 1.0000000
## LA1511_S_noga_9-LA1511_S_higa_9  0.0284848485 -0.43363447 0.49060417 1.0000000
## M058_C_higa_9-LA1511_S_higa_9    0.1658181818 -0.28341314 0.61504951 0.9977445
## M058_C_loga_9-LA1511_S_higa_9    0.0408181818 -0.40841314 0.49004951 1.0000000
## M058_C_noga_9-LA1511_S_higa_9    0.2088181818 -0.24041314 0.65804951 0.9730767
## M058_S_higa_9-LA1511_S_higa_9    0.2478181818 -0.20141314 0.69704951 0.8850277
## M058_S_loga_9-LA1511_S_higa_9    0.2618181818 -0.18741314 0.71104951 0.8309745
## M058_S_noga_9-LA1511_S_higa_9    0.3618181818 -0.10030114 0.82393750 0.3386526
## M248_C_higa_9-LA1511_S_higa_9    0.1088181818 -0.34041314 0.55804951 0.9999920
## M248_C_loga_9-LA1511_S_higa_9    0.0788181818 -0.37041314 0.52804951 0.9999999
## M248_C_noga_9-LA1511_S_higa_9    0.0708181818 -0.37841314 0.52004951 1.0000000
## M248_S_higa_9-LA1511_S_higa_9    0.0298181818 -0.41941314 0.47904951 1.0000000
## M248_S_loga_9-LA1511_S_higa_9   -0.0641818182 -0.51341314 0.38504951 1.0000000
## M248_S_noga_9-LA1511_S_higa_9    0.0148181818 -0.43441314 0.46404951 1.0000000
## LA1511_S_noga_9-LA1511_S_loga_9  0.0784848485 -0.38363447 0.54060417 1.0000000
## M058_C_higa_9-LA1511_S_loga_9    0.2158181818 -0.23341314 0.66504951 0.9633768
## M058_C_loga_9-LA1511_S_loga_9    0.0908181818 -0.35841314 0.54004951 0.9999995
## M058_C_noga_9-LA1511_S_loga_9    0.2588181818 -0.19041314 0.70804951 0.8435676
## M058_S_higa_9-LA1511_S_loga_9    0.2978181818 -0.15141314 0.74704951 0.6454022
## M058_S_loga_9-LA1511_S_loga_9    0.3118181818 -0.13741314 0.76104951 0.5630832
## M058_S_noga_9-LA1511_S_loga_9    0.4118181818 -0.05030114 0.87393750 0.1455346
## M248_C_higa_9-LA1511_S_loga_9    0.1588181818 -0.29041314 0.60804951 0.9986593
## M248_C_loga_9-LA1511_S_loga_9    0.1288181818 -0.32041314 0.57804951 0.9999122
## M248_C_noga_9-LA1511_S_loga_9    0.1208181818 -0.32841314 0.57004951 0.9999640
## M248_S_higa_9-LA1511_S_loga_9    0.0798181818 -0.36941314 0.52904951 0.9999999
## M248_S_loga_9-LA1511_S_loga_9   -0.0141818182 -0.46341314 0.43504951 1.0000000
## M248_S_noga_9-LA1511_S_loga_9    0.0648181818 -0.38441314 0.51404951 1.0000000
## M058_C_higa_9-LA1511_S_noga_9    0.1373333333 -0.33506926 0.60973593 0.9998941
## M058_C_loga_9-LA1511_S_noga_9    0.0123333333 -0.46006926 0.48473593 1.0000000
## M058_C_noga_9-LA1511_S_noga_9    0.1803333333 -0.29206926 0.65273593 0.9966548
## M058_S_higa_9-LA1511_S_noga_9    0.2193333333 -0.25306926 0.69173593 0.9733740
## M058_S_loga_9-LA1511_S_noga_9    0.2333333333 -0.23906926 0.70573593 0.9530325
## M058_S_noga_9-LA1511_S_noga_9    0.3333333333 -0.15134150 0.81800817 0.5800378
## M248_C_higa_9-LA1511_S_noga_9    0.0803333333 -0.39206926 0.55273593 1.0000000
## M248_C_loga_9-LA1511_S_noga_9    0.0503333333 -0.42206926 0.52273593 1.0000000
## M248_C_noga_9-LA1511_S_noga_9    0.0423333333 -0.43006926 0.51473593 1.0000000
## M248_S_higa_9-LA1511_S_noga_9    0.0013333333 -0.47106926 0.47373593 1.0000000
## M248_S_loga_9-LA1511_S_noga_9   -0.0926666667 -0.56506926 0.37973593 0.9999997
## M248_S_noga_9-LA1511_S_noga_9   -0.0136666667 -0.48606926 0.45873593 1.0000000
## M058_C_loga_9-M058_C_higa_9     -0.1250000000 -0.58480292 0.33480292 0.9999581
## M058_C_noga_9-M058_C_higa_9      0.0430000000 -0.41680292 0.50280292 1.0000000
## M058_S_higa_9-M058_C_higa_9      0.0820000000 -0.37780292 0.54180292 0.9999999
## M058_S_loga_9-M058_C_higa_9      0.0960000000 -0.36380292 0.55580292 0.9999991
## M058_S_noga_9-M058_C_higa_9      0.1960000000 -0.27640259 0.66840259 0.9915126
## M248_C_higa_9-M058_C_higa_9     -0.0570000000 -0.51680292 0.40280292 1.0000000
## M248_C_loga_9-M058_C_higa_9     -0.0870000000 -0.54680292 0.37280292 0.9999998
## M248_C_noga_9-M058_C_higa_9     -0.0950000000 -0.55480292 0.36480292 0.9999993
## M248_S_higa_9-M058_C_higa_9     -0.1360000000 -0.59580292 0.32380292 0.9998661
## M248_S_loga_9-M058_C_higa_9     -0.2300000000 -0.68980292 0.22980292 0.9475563
## M248_S_noga_9-M058_C_higa_9     -0.1510000000 -0.61080292 0.30880292 0.9994680
## M058_C_noga_9-M058_C_loga_9      0.1680000000 -0.29180292 0.62780292 0.9980024
## M058_S_higa_9-M058_C_loga_9      0.2070000000 -0.25280292 0.66680292 0.9802675
## M058_S_loga_9-M058_C_loga_9      0.2210000000 -0.23880292 0.68080292 0.9632205
## M058_S_noga_9-M058_C_loga_9      0.3210000000 -0.15140259 0.79340259 0.6019181
## M248_C_higa_9-M058_C_loga_9      0.0680000000 -0.39180292 0.52780292 1.0000000
## M248_C_loga_9-M058_C_loga_9      0.0380000000 -0.42180292 0.49780292 1.0000000
## M248_C_noga_9-M058_C_loga_9      0.0300000000 -0.42980292 0.48980292 1.0000000
## M248_S_higa_9-M058_C_loga_9     -0.0110000000 -0.47080292 0.44880292 1.0000000
## M248_S_loga_9-M058_C_loga_9     -0.1050000000 -0.56480292 0.35480292 0.9999966
## M248_S_noga_9-M058_C_loga_9     -0.0260000000 -0.48580292 0.43380292 1.0000000
## M058_S_higa_9-M058_C_noga_9      0.0390000000 -0.42080292 0.49880292 1.0000000
## M058_S_loga_9-M058_C_noga_9      0.0530000000 -0.40680292 0.51280292 1.0000000
## M058_S_noga_9-M058_C_noga_9      0.1530000000 -0.31940259 0.62540259 0.9995550
## M248_C_higa_9-M058_C_noga_9     -0.1000000000 -0.55980292 0.35980292 0.9999984
## M248_C_loga_9-M058_C_noga_9     -0.1300000000 -0.58980292 0.32980292 0.9999277
## M248_C_noga_9-M058_C_noga_9     -0.1380000000 -0.59780292 0.32180292 0.9998369
## M248_S_higa_9-M058_C_noga_9     -0.1790000000 -0.63880292 0.28080292 0.9958099
## M248_S_loga_9-M058_C_noga_9     -0.2730000000 -0.73280292 0.18680292 0.8092555
## M248_S_noga_9-M058_C_noga_9     -0.1940000000 -0.65380292 0.26580292 0.9898473
## M058_S_loga_9-M058_S_higa_9      0.0140000000 -0.44580292 0.47380292 1.0000000
## M058_S_noga_9-M058_S_higa_9      0.1140000000 -0.35840259 0.58640259 0.9999924
## M248_C_higa_9-M058_S_higa_9     -0.1390000000 -0.59880292 0.32080292 0.9998203
## M248_C_loga_9-M058_S_higa_9     -0.1690000000 -0.62880292 0.29080292 0.9978558
## M248_C_noga_9-M058_S_higa_9     -0.1770000000 -0.63680292 0.28280292 0.9963154
## M248_S_higa_9-M058_S_higa_9     -0.2180000000 -0.67780292 0.24180292 0.9675717
## M248_S_loga_9-M058_S_higa_9     -0.3120000000 -0.77180292 0.14780292 0.6044426
## M248_S_noga_9-M058_S_higa_9     -0.2330000000 -0.69280292 0.22680292 0.9414017
## M058_S_noga_9-M058_S_loga_9      0.1000000000 -0.37240259 0.57240259 0.9999989
## M248_C_higa_9-M058_S_loga_9     -0.1530000000 -0.61280292 0.30680292 0.9993706
## M248_C_loga_9-M058_S_loga_9     -0.1830000000 -0.64280292 0.27680292 0.9946230
## M248_C_noga_9-M058_S_loga_9     -0.1910000000 -0.65080292 0.26880292 0.9914030
## M248_S_higa_9-M058_S_loga_9     -0.2320000000 -0.69180292 0.22780292 0.9435074
## M248_S_loga_9-M058_S_loga_9     -0.3260000000 -0.78580292 0.13380292 0.5234913
## M248_S_noga_9-M058_S_loga_9     -0.2470000000 -0.70680292 0.21280292 0.9059422
## M248_C_higa_9-M058_S_noga_9     -0.2530000000 -0.72540259 0.21940259 0.9081276
## M248_C_loga_9-M058_S_noga_9     -0.2830000000 -0.75540259 0.18940259 0.7981591
## M248_C_noga_9-M058_S_noga_9     -0.2910000000 -0.76340259 0.18140259 0.7609467
## M248_S_higa_9-M058_S_noga_9     -0.3320000000 -0.80440259 0.14040259 0.5399851
## M248_S_loga_9-M058_S_noga_9     -0.4260000000 -0.89840259 0.04640259 0.1323236
## M248_S_noga_9-M058_S_noga_9     -0.3470000000 -0.81940259 0.12540259 0.4565874
## M248_C_loga_9-M248_C_higa_9     -0.0300000000 -0.48980292 0.42980292 1.0000000
## M248_C_noga_9-M248_C_higa_9     -0.0380000000 -0.49780292 0.42180292 1.0000000
## M248_S_higa_9-M248_C_higa_9     -0.0790000000 -0.53880292 0.38080292 1.0000000
## M248_S_loga_9-M248_C_higa_9     -0.1730000000 -0.63280292 0.28680292 0.9971736
## M248_S_noga_9-M248_C_higa_9     -0.0940000000 -0.55380292 0.36580292 0.9999994
## M248_C_noga_9-M248_C_loga_9     -0.0080000000 -0.46780292 0.45180292 1.0000000
## M248_S_higa_9-M248_C_loga_9     -0.0490000000 -0.50880292 0.41080292 1.0000000
## M248_S_loga_9-M248_C_loga_9     -0.1430000000 -0.60280292 0.31680292 0.9997380
## M248_S_noga_9-M248_C_loga_9     -0.0640000000 -0.52380292 0.39580292 1.0000000
## M248_S_higa_9-M248_C_noga_9     -0.0410000000 -0.50080292 0.41880292 1.0000000
## M248_S_loga_9-M248_C_noga_9     -0.1350000000 -0.59480292 0.32480292 0.9998788
## M248_S_noga_9-M248_C_noga_9     -0.0560000000 -0.51580292 0.40380292 1.0000000
## M248_S_loga_9-M248_S_higa_9     -0.0940000000 -0.55380292 0.36580292 0.9999994
## M248_S_noga_9-M248_S_higa_9     -0.0150000000 -0.47480292 0.44480292 1.0000000
## M248_S_noga_9-M248_S_loga_9      0.0790000000 -0.38080292 0.53880292 1.0000000
P6 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P6)
stat.test
## $Letters
## LA1511_C_loga_9 LA1511_C_noga_9 LA1511_S_higa_9 LA1511_S_loga_9 LA1511_S_noga_9 
##             "a"             "a"             "a"             "a"             "a" 
##   M058_C_higa_9   M058_C_loga_9   M058_C_noga_9   M058_S_higa_9   M058_S_loga_9 
##             "a"             "a"             "a"             "a"             "a" 
##   M058_S_noga_9   M248_C_higa_9   M248_C_loga_9   M248_C_noga_9   M248_S_higa_9 
##             "a"             "a"             "a"             "a"             "a" 
##   M248_S_loga_9   M248_S_noga_9 LA1511_C_higa_9 
##             "a"             "a"             "a" 
## 
## $LetterMatrix
##                    a
## LA1511_C_loga_9 TRUE
## LA1511_C_noga_9 TRUE
## LA1511_S_higa_9 TRUE
## LA1511_S_loga_9 TRUE
## LA1511_S_noga_9 TRUE
## M058_C_higa_9   TRUE
## M058_C_loga_9   TRUE
## M058_C_noga_9   TRUE
## M058_S_higa_9   TRUE
## M058_S_loga_9   TRUE
## M058_S_noga_9   TRUE
## M248_C_higa_9   TRUE
## M248_C_loga_9   TRUE
## M248_C_noga_9   TRUE
## M248_S_higa_9   TRUE
## M248_S_loga_9   TRUE
## M248_S_noga_9   TRUE
## LA1511_C_higa_9 TRUE
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
GA_pareto_location2$Condition.all <- factor(GA_pareto_location2$Condition.all, levels = c("C_noga", "C_loga","C_higa",  "S_noga","S_loga","S_higa"))

GA_pareto_location_graph <- ggplot(data = GA_pareto_location2, mapping = aes(x = All.ID, y = pareto.front.scaling.location
, colour = Condition.all)) 
GA_pareto_location_graph<- GA_pareto_location_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
GA_pareto_location_graph <- GA_pareto_location_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
GA_pareto_location_graph <- GA_pareto_location_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
GA_pareto_location_graph <- GA_pareto_location_graph + ylab("Pareto front location") + xlab("") #+ ggtitle("")
GA_pareto_location_graph <- GA_pareto_location_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
GA_pareto_location_graph <- GA_pareto_location_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 1.5)
GA_pareto_location_graph

GA_pareto_location_graph <- ggplot(data=GA_pareto_location2, aes(x= Condition.all, y=pareto.front.scaling.location, color = Condition.all)) 
GA_pareto_location_graph <- GA_pareto_location_graph +  geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
GA_pareto_location_graph <- GA_pareto_location_graph + facet_grid(~ Accessions )

GA_pareto_location_graph <- GA_pareto_location_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
GA_pareto_location_graph <- GA_pareto_location_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
GA_pareto_location_graph <- GA_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))
GA_pareto_location_graph

aov(pareto.front.scaling.distance ~ All.ID, data = GA_pareto_location2)
## Call:
##    aov(formula = pareto.front.scaling.distance ~ All.ID, data = GA_pareto_location2)
## 
## Terms:
##                    All.ID Residuals
## Sum of Squares   1.815824 21.760736
## Deg. of Freedom        17       163
## 
## Residual standard error: 0.3653785
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.scaling.distance ~ All.ID, data = GA_pareto_location2))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = pareto.front.scaling.distance ~ All.ID, data = GA_pareto_location2)
## 
## $All.ID
##                                         diff        lwr       upr     p adj
## LA1511_C_loga_9-LA1511_C_higa_9  0.241240682 -0.3248165 0.8072979 0.9887141
## LA1511_C_noga_9-LA1511_C_higa_9 -0.061119318 -0.6271765 0.5049379 1.0000000
## LA1511_S_higa_9-LA1511_C_higa_9 -0.037399545 -0.5898148 0.5150157 1.0000000
## LA1511_S_loga_9-LA1511_C_higa_9  0.269640000 -0.2827753 0.8220553 0.9577193
## LA1511_S_noga_9-LA1511_C_higa_9  0.037098737 -0.5451981 0.6193955 1.0000000
## M058_C_higa_9-LA1511_C_higa_9   -0.058766418 -0.6248236 0.5072908 1.0000000
## M058_C_loga_9-LA1511_C_higa_9    0.082971082 -0.4830861 0.6490283 1.0000000
## M058_C_noga_9-LA1511_C_higa_9   -0.042789918 -0.6088471 0.5232673 1.0000000
## M058_S_higa_9-LA1511_C_higa_9   -0.035723918 -0.6017811 0.5303333 1.0000000
## M058_S_loga_9-LA1511_C_higa_9   -0.009364718 -0.5754219 0.5566925 1.0000000
## M058_S_noga_9-LA1511_C_higa_9    0.029128737 -0.5531681 0.6114255 1.0000000
## M248_C_higa_9-LA1511_C_higa_9   -0.067374618 -0.6334318 0.4986826 1.0000000
## M248_C_loga_9-LA1511_C_higa_9   -0.065548218 -0.6316054 0.5005090 1.0000000
## M248_C_noga_9-LA1511_C_higa_9   -0.046914918 -0.6129721 0.5191423 1.0000000
## M248_S_higa_9-LA1511_C_higa_9    0.022433982 -0.5436232 0.5884912 1.0000000
## M248_S_loga_9-LA1511_C_higa_9   -0.069803818 -0.6358610 0.4962534 1.0000000
## M248_S_noga_9-LA1511_C_higa_9   -0.083617918 -0.6496751 0.4824393 1.0000000
## LA1511_C_noga_9-LA1511_C_loga_9 -0.302360000 -0.8817380 0.2770180 0.9252027
## LA1511_S_higa_9-LA1511_C_loga_9 -0.278640227 -0.8446974 0.2874170 0.9544243
## LA1511_S_loga_9-LA1511_C_loga_9  0.028399318 -0.5376579 0.5944565 1.0000000
## LA1511_S_noga_9-LA1511_C_loga_9 -0.204141944 -0.7993963 0.3911124 0.9990793
## M058_C_higa_9-LA1511_C_loga_9   -0.300007100 -0.8793851 0.2793709 0.9298210
## M058_C_loga_9-LA1511_C_loga_9   -0.158269600 -0.7376476 0.4211084 0.9999552
## M058_C_noga_9-LA1511_C_loga_9   -0.284030600 -0.8634086 0.2953474 0.9560511
## M058_S_higa_9-LA1511_C_loga_9   -0.276964600 -0.8563426 0.3024134 0.9650058
## M058_S_loga_9-LA1511_C_loga_9   -0.250605400 -0.8299834 0.3287726 0.9868312
## M058_S_noga_9-LA1511_C_loga_9   -0.212111944 -0.8073663 0.3831424 0.9985235
## M248_C_higa_9-LA1511_C_loga_9   -0.308615300 -0.8879933 0.2707627 0.9119326
## M248_C_loga_9-LA1511_C_loga_9   -0.306788900 -0.8861669 0.2725891 0.9159577
## M248_C_noga_9-LA1511_C_loga_9   -0.288155600 -0.8675336 0.2912224 0.9501031
## M248_S_higa_9-LA1511_C_loga_9   -0.218806700 -0.7981847 0.3605713 0.9970473
## M248_S_loga_9-LA1511_C_loga_9   -0.311044500 -0.8904225 0.2683335 0.9063847
## M248_S_noga_9-LA1511_C_loga_9   -0.324858600 -0.9042366 0.2545194 0.8705783
## LA1511_S_higa_9-LA1511_C_noga_9  0.023719773 -0.5423374 0.5897770 1.0000000
## LA1511_S_loga_9-LA1511_C_noga_9  0.330759318 -0.2352979 0.8968165 0.8280579
## LA1511_S_noga_9-LA1511_C_noga_9  0.098218056 -0.4970363 0.6934724 1.0000000
## M058_C_higa_9-LA1511_C_noga_9    0.002352900 -0.5770251 0.5817309 1.0000000
## M058_C_loga_9-LA1511_C_noga_9    0.144090400 -0.4352876 0.7234684 0.9999882
## M058_C_noga_9-LA1511_C_noga_9    0.018329400 -0.5610486 0.5977074 1.0000000
## M058_S_higa_9-LA1511_C_noga_9    0.025395400 -0.5539826 0.6047734 1.0000000
## M058_S_loga_9-LA1511_C_noga_9    0.051754600 -0.5276234 0.6311326 1.0000000
## M058_S_noga_9-LA1511_C_noga_9    0.090248056 -0.5050063 0.6855024 1.0000000
## M248_C_higa_9-LA1511_C_noga_9   -0.006255300 -0.5856333 0.5731227 1.0000000
## M248_C_loga_9-LA1511_C_noga_9   -0.004428900 -0.5838069 0.5749491 1.0000000
## M248_C_noga_9-LA1511_C_noga_9    0.014204400 -0.5651736 0.5935824 1.0000000
## M248_S_higa_9-LA1511_C_noga_9    0.083553300 -0.4958247 0.6629313 1.0000000
## M248_S_loga_9-LA1511_C_noga_9   -0.008684500 -0.5880625 0.5706935 1.0000000
## M248_S_noga_9-LA1511_C_noga_9   -0.022498600 -0.6018766 0.5568794 1.0000000
## LA1511_S_loga_9-LA1511_S_higa_9  0.307039545 -0.2453757 0.8594548 0.8785117
## LA1511_S_noga_9-LA1511_S_higa_9  0.074498283 -0.5077985 0.6567951 1.0000000
## M058_C_higa_9-LA1511_S_higa_9   -0.021366873 -0.5874241 0.5446903 1.0000000
## M058_C_loga_9-LA1511_S_higa_9    0.120370627 -0.4456866 0.6864278 0.9999988
## M058_C_noga_9-LA1511_S_higa_9   -0.005390373 -0.5714476 0.5606668 1.0000000
## M058_S_higa_9-LA1511_S_higa_9    0.001675627 -0.5643816 0.5677328 1.0000000
## M058_S_loga_9-LA1511_S_higa_9    0.028034827 -0.5380224 0.5940920 1.0000000
## M058_S_noga_9-LA1511_S_higa_9    0.066528283 -0.5157685 0.6488251 1.0000000
## M248_C_higa_9-LA1511_S_higa_9   -0.029975073 -0.5960323 0.5360821 1.0000000
## M248_C_loga_9-LA1511_S_higa_9   -0.028148673 -0.5942059 0.5379085 1.0000000
## M248_C_noga_9-LA1511_S_higa_9   -0.009515373 -0.5755726 0.5565418 1.0000000
## M248_S_higa_9-LA1511_S_higa_9    0.059833527 -0.5062237 0.6258907 1.0000000
## M248_S_loga_9-LA1511_S_higa_9   -0.032404273 -0.5984615 0.5336529 1.0000000
## M248_S_noga_9-LA1511_S_higa_9   -0.046218373 -0.6122756 0.5198388 1.0000000
## LA1511_S_noga_9-LA1511_S_loga_9 -0.232541263 -0.8148381 0.3497555 0.9944151
## M058_C_higa_9-LA1511_S_loga_9   -0.328406418 -0.8944636 0.2376508 0.8360338
## M058_C_loga_9-LA1511_S_loga_9   -0.186668918 -0.7527261 0.3793883 0.9994389
## M058_C_noga_9-LA1511_S_loga_9   -0.312429918 -0.8784871 0.2536273 0.8845792
## M058_S_higa_9-LA1511_S_loga_9   -0.305363918 -0.8714211 0.2606933 0.9028346
## M058_S_loga_9-LA1511_S_loga_9   -0.279004718 -0.8450619 0.2870525 0.9538949
## M058_S_noga_9-LA1511_S_loga_9   -0.240511263 -0.8228081 0.3417855 0.9919145
## M248_C_higa_9-LA1511_S_loga_9   -0.337014618 -0.9030718 0.2290426 0.8058775
## M248_C_loga_9-LA1511_S_loga_9   -0.335188218 -0.9012454 0.2308690 0.8124972
## M248_C_noga_9-LA1511_S_loga_9   -0.316554918 -0.8826121 0.2495023 0.8730028
## M248_S_higa_9-LA1511_S_loga_9   -0.247206018 -0.8132632 0.3188512 0.9854653
## M248_S_loga_9-LA1511_S_loga_9   -0.339443818 -0.9055010 0.2266134 0.7968951
## M248_S_noga_9-LA1511_S_loga_9   -0.353257918 -0.9193151 0.2127993 0.7422514
## M058_C_higa_9-LA1511_S_noga_9   -0.095865156 -0.6911195 0.4993892 1.0000000
## M058_C_loga_9-LA1511_S_noga_9    0.045872344 -0.5493820 0.6411267 1.0000000
## M058_C_noga_9-LA1511_S_noga_9   -0.079888656 -0.6751430 0.5153657 1.0000000
## M058_S_higa_9-LA1511_S_noga_9   -0.072822656 -0.6680770 0.5224317 1.0000000
## M058_S_loga_9-LA1511_S_noga_9   -0.046463456 -0.6417178 0.5487909 1.0000000
## M058_S_noga_9-LA1511_S_noga_9   -0.007970000 -0.6186880 0.6027480 1.0000000
## M248_C_higa_9-LA1511_S_noga_9   -0.104473356 -0.6997277 0.4907810 0.9999999
## M248_C_loga_9-LA1511_S_noga_9   -0.102646956 -0.6979013 0.4926074 1.0000000
## M248_C_noga_9-LA1511_S_noga_9   -0.084013656 -0.6792680 0.5112407 1.0000000
## M248_S_higa_9-LA1511_S_noga_9   -0.014664756 -0.6099191 0.5805896 1.0000000
## M248_S_loga_9-LA1511_S_noga_9   -0.106902556 -0.7021569 0.4883518 0.9999999
## M248_S_noga_9-LA1511_S_noga_9   -0.120716656 -0.7159710 0.4745377 0.9999994
## M058_C_loga_9-M058_C_higa_9      0.141737500 -0.4376405 0.7211155 0.9999907
## M058_C_noga_9-M058_C_higa_9      0.015976500 -0.5634015 0.5953545 1.0000000
## M058_S_higa_9-M058_C_higa_9      0.023042500 -0.5563355 0.6024205 1.0000000
## M058_S_loga_9-M058_C_higa_9      0.049401700 -0.5299763 0.6287797 1.0000000
## M058_S_noga_9-M058_C_higa_9      0.087895156 -0.5073592 0.6831495 1.0000000
## M248_C_higa_9-M058_C_higa_9     -0.008608200 -0.5879862 0.5707698 1.0000000
## M248_C_loga_9-M058_C_higa_9     -0.006781800 -0.5861598 0.5725962 1.0000000
## M248_C_noga_9-M058_C_higa_9      0.011851500 -0.5675265 0.5912295 1.0000000
## M248_S_higa_9-M058_C_higa_9      0.081200400 -0.4981776 0.6605784 1.0000000
## M248_S_loga_9-M058_C_higa_9     -0.011037400 -0.5904154 0.5683406 1.0000000
## M248_S_noga_9-M058_C_higa_9     -0.024851500 -0.6042295 0.5545265 1.0000000
## M058_C_noga_9-M058_C_loga_9     -0.125761000 -0.7051390 0.4536170 0.9999984
## M058_S_higa_9-M058_C_loga_9     -0.118695000 -0.6980730 0.4606830 0.9999993
## M058_S_loga_9-M058_C_loga_9     -0.092335800 -0.6717138 0.4870422 1.0000000
## M058_S_noga_9-M058_C_loga_9     -0.053842344 -0.6490967 0.5414120 1.0000000
## M248_C_higa_9-M058_C_loga_9     -0.150345700 -0.7297237 0.4290323 0.9999783
## M248_C_loga_9-M058_C_loga_9     -0.148519300 -0.7278973 0.4308587 0.9999818
## M248_C_noga_9-M058_C_loga_9     -0.129886000 -0.7092640 0.4494920 0.9999974
## M248_S_higa_9-M058_C_loga_9     -0.060537100 -0.6399151 0.5188409 1.0000000
## M248_S_loga_9-M058_C_loga_9     -0.152774900 -0.7321529 0.4266031 0.9999728
## M248_S_noga_9-M058_C_loga_9     -0.166589000 -0.7459670 0.4127890 0.9999089
## M058_S_higa_9-M058_C_noga_9      0.007066000 -0.5723120 0.5864440 1.0000000
## M058_S_loga_9-M058_C_noga_9      0.033425200 -0.5459528 0.6128032 1.0000000
## M058_S_noga_9-M058_C_noga_9      0.071918656 -0.5233357 0.6671730 1.0000000
## M248_C_higa_9-M058_C_noga_9     -0.024584700 -0.6039627 0.5547933 1.0000000
## M248_C_loga_9-M058_C_noga_9     -0.022758300 -0.6021363 0.5566197 1.0000000
## M248_C_noga_9-M058_C_noga_9     -0.004125000 -0.5835030 0.5752530 1.0000000
## M248_S_higa_9-M058_C_noga_9      0.065223900 -0.5141541 0.6446019 1.0000000
## M248_S_loga_9-M058_C_noga_9     -0.027013900 -0.6063919 0.5523641 1.0000000
## M248_S_noga_9-M058_C_noga_9     -0.040828000 -0.6202060 0.5385500 1.0000000
## M058_S_loga_9-M058_S_higa_9      0.026359200 -0.5530188 0.6057372 1.0000000
## M058_S_noga_9-M058_S_higa_9      0.064852656 -0.5304017 0.6601070 1.0000000
## M248_C_higa_9-M058_S_higa_9     -0.031650700 -0.6110287 0.5477273 1.0000000
## M248_C_loga_9-M058_S_higa_9     -0.029824300 -0.6092023 0.5495537 1.0000000
## M248_C_noga_9-M058_S_higa_9     -0.011191000 -0.5905690 0.5681870 1.0000000
## M248_S_higa_9-M058_S_higa_9      0.058157900 -0.5212201 0.6375359 1.0000000
## M248_S_loga_9-M058_S_higa_9     -0.034079900 -0.6134579 0.5452981 1.0000000
## M248_S_noga_9-M058_S_higa_9     -0.047894000 -0.6272720 0.5314840 1.0000000
## M058_S_noga_9-M058_S_loga_9      0.038493456 -0.5567609 0.6337478 1.0000000
## M248_C_higa_9-M058_S_loga_9     -0.058009900 -0.6373879 0.5213681 1.0000000
## M248_C_loga_9-M058_S_loga_9     -0.056183500 -0.6355615 0.5231945 1.0000000
## M248_C_noga_9-M058_S_loga_9     -0.037550200 -0.6169282 0.5418278 1.0000000
## M248_S_higa_9-M058_S_loga_9      0.031798700 -0.5475793 0.6111767 1.0000000
## M248_S_loga_9-M058_S_loga_9     -0.060439100 -0.6398171 0.5189389 1.0000000
## M248_S_noga_9-M058_S_loga_9     -0.074253200 -0.6536312 0.5051248 1.0000000
## M248_C_higa_9-M058_S_noga_9     -0.096503356 -0.6917577 0.4987510 1.0000000
## M248_C_loga_9-M058_S_noga_9     -0.094676956 -0.6899313 0.5005774 1.0000000
## M248_C_noga_9-M058_S_noga_9     -0.076043656 -0.6712980 0.5192107 1.0000000
## M248_S_higa_9-M058_S_noga_9     -0.006694756 -0.6019491 0.5885596 1.0000000
## M248_S_loga_9-M058_S_noga_9     -0.098932556 -0.6941869 0.4963218 1.0000000
## M248_S_noga_9-M058_S_noga_9     -0.112746656 -0.7080010 0.4825077 0.9999998
## M248_C_loga_9-M248_C_higa_9      0.001826400 -0.5775516 0.5812044 1.0000000
## M248_C_noga_9-M248_C_higa_9      0.020459700 -0.5589183 0.5998377 1.0000000
## M248_S_higa_9-M248_C_higa_9      0.089808600 -0.4895694 0.6691866 1.0000000
## M248_S_loga_9-M248_C_higa_9     -0.002429200 -0.5818072 0.5769488 1.0000000
## M248_S_noga_9-M248_C_higa_9     -0.016243300 -0.5956213 0.5631347 1.0000000
## M248_C_noga_9-M248_C_loga_9      0.018633300 -0.5607447 0.5980113 1.0000000
## M248_S_higa_9-M248_C_loga_9      0.087982200 -0.4913958 0.6673602 1.0000000
## M248_S_loga_9-M248_C_loga_9     -0.004255600 -0.5836336 0.5751224 1.0000000
## M248_S_noga_9-M248_C_loga_9     -0.018069700 -0.5974477 0.5613083 1.0000000
## M248_S_higa_9-M248_C_noga_9      0.069348900 -0.5100291 0.6487269 1.0000000
## M248_S_loga_9-M248_C_noga_9     -0.022888900 -0.6022669 0.5564891 1.0000000
## M248_S_noga_9-M248_C_noga_9     -0.036703000 -0.6160810 0.5426750 1.0000000
## M248_S_loga_9-M248_S_higa_9     -0.092237800 -0.6716158 0.4871402 1.0000000
## M248_S_noga_9-M248_S_higa_9     -0.106051900 -0.6854299 0.4733261 0.9999999
## M248_S_noga_9-M248_S_loga_9     -0.013814100 -0.5931921 0.5655639 1.0000000
P5 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P5)
stat.test
## $Letters
## LA1511_C_loga_9 LA1511_C_noga_9 LA1511_S_higa_9 LA1511_S_loga_9 LA1511_S_noga_9 
##             "a"             "a"             "a"             "a"             "a" 
##   M058_C_higa_9   M058_C_loga_9   M058_C_noga_9   M058_S_higa_9   M058_S_loga_9 
##             "a"             "a"             "a"             "a"             "a" 
##   M058_S_noga_9   M248_C_higa_9   M248_C_loga_9   M248_C_noga_9   M248_S_higa_9 
##             "a"             "a"             "a"             "a"             "a" 
##   M248_S_loga_9   M248_S_noga_9 LA1511_C_higa_9 
##             "a"             "a"             "a" 
## 
## $LetterMatrix
##                    a
## LA1511_C_loga_9 TRUE
## LA1511_C_noga_9 TRUE
## LA1511_S_higa_9 TRUE
## LA1511_S_loga_9 TRUE
## LA1511_S_noga_9 TRUE
## M058_C_higa_9   TRUE
## M058_C_loga_9   TRUE
## M058_C_noga_9   TRUE
## M058_S_higa_9   TRUE
## M058_S_loga_9   TRUE
## M058_S_noga_9   TRUE
## M248_C_higa_9   TRUE
## M248_C_loga_9   TRUE
## M248_C_noga_9   TRUE
## M248_S_higa_9   TRUE
## M248_S_loga_9   TRUE
## M248_S_noga_9   TRUE
## LA1511_C_higa_9 TRUE
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
GA_pareto_location3 <- subset(GA_pareto_location2, GA_pareto_location2$pareto.front.scaling.distanc < 2)

GA_pareto_distance_graph <- ggplot(data = GA_pareto_location3, mapping = aes(x = All.ID, y = pareto.front.scaling.distance
, colour = Condition.all)) 
GA_pareto_distance_graph <- GA_pareto_distance_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
GA_pareto_distance_graph <- GA_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
GA_pareto_distance_graph <- GA_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
GA_pareto_distance_graph <- GA_pareto_distance_graph + ylab("Pareto front scaling distance") + xlab("") #+ ggtitle("")
GA_pareto_distance_graph <- GA_pareto_distance_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
GA_pareto_distance_graph <- GA_pareto_distance_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 2.5)
GA_pareto_distance_graph

GA_pareto_distance_graph <- ggplot(data=GA_pareto_location3, aes(x= Condition.all, y=pareto.front.scaling.distance, color = Condition.all)) 
GA_pareto_distance_graph <- GA_pareto_distance_graph +  geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
GA_pareto_distance_graph <- GA_pareto_distance_graph + facet_grid(~ Accessions )

GA_pareto_distance_graph <- GA_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
GA_pareto_distance_graph <- GA_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
GA_pareto_distance_graph <- GA_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))
GA_pareto_distance_graph