This is a pareto-front components calculation for 3 tomatoes experienced ACC and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220620_RSA_M248M058LA1511_ACC_100mM_Salt. The root tracing was done by Stacey Na in April 2023.

getwd()
## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20230518_ACC_pareto-front_components"
list.files(pattern = ".csv")
## [1] "ACC-pareto-scaling_nonscaling_analysis.csv"
ACC_pareto_location <-read.csv("ACC-pareto-scaling_nonscaling_analysis.csv")
ACC_pareto_location
ACC_pareto_location$Accessions <- gsub("M058", "m058", ACC_pareto_location$Accessions)

ACC_pareto_location$Condition.all <- paste(ACC_pareto_location$Condition, ACC_pareto_location$Condition2, sep="_")
ACC_pareto_location
library(ggplot2)
library(ggpubr)
library(multcompView)
ACC_pareto_location$All.ID <- paste(ACC_pareto_location$Accessions, ACC_pareto_location$Condition.all, ACC_pareto_location$Day, sep="_")
ACC_pareto_location
ACC_pareto_location2 <- subset(ACC_pareto_location, ACC_pareto_location$Day > 5)
ACC_pareto_location2
aov(pareto.front.scaling.location ~ All.ID, data = ACC_pareto_location2)
## Call:
##    aov(formula = pareto.front.scaling.location ~ All.ID, data = ACC_pareto_location2)
## 
## Terms:
##                   All.ID Residuals
## Sum of Squares  1.998107  3.089923
## Deg. of Freedom       17       139
## 
## Residual standard error: 0.1490962
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.scaling.location ~ All.ID, data = ACC_pareto_location2))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = pareto.front.scaling.location ~ All.ID, data = ACC_pareto_location2)
## 
## $All.ID
##                                            diff         lwr          upr
## la1511_C_5acc_9-la1511_C_1acc_9   -7.166667e-02 -0.36660223  0.223268900
## la1511_C_noacc_9-la1511_C_1acc_9  -1.888095e-01 -0.48374509  0.106126043
## la1511_S_1acc_9-la1511_C_1acc_9    2.300000e-01 -0.07606910  0.536069103
## la1511_S_5acc_9-la1511_C_1acc_9   -1.383333e-01 -0.44440244  0.167735769
## la1511_S_noacc_9-la1511_C_1acc_9  -1.888095e-01 -0.48374509  0.106126043
## m058_C_1acc_9-la1511_C_1acc_9      8.611111e-02 -0.19329047  0.365512697
## m058_C_5acc_9-la1511_C_1acc_9     -3.766667e-02 -0.31142319  0.236089861
## m058_C_noacc_9-la1511_C_1acc_9     1.503333e-01 -0.12342319  0.424089861
## m058_S_1acc_9-la1511_C_1acc_9      4.333333e-02 -0.23042319  0.317089861
## m058_S_5acc_9-la1511_C_1acc_9     -1.156667e-01 -0.38942319  0.158089861
## m058_S_noacc_9-la1511_C_1acc_9     4.933333e-02 -0.22442319  0.323089861
## m248_C_1acc_9-la1511_C_1acc_9      1.073333e-01 -0.16642319  0.381089861
## m248_C_5acc_9-la1511_C_1acc_9     -3.666667e-03 -0.27742319  0.270089861
## m248_C_noacc_9-la1511_C_1acc_9     1.133333e-02 -0.26242319  0.285089861
## m248_S_1acc_9-la1511_C_1acc_9      1.238889e-01 -0.15551270  0.403290475
## m248_S_5acc_9-la1511_C_1acc_9     -5.366667e-02 -0.32742319  0.220089861
## m248_S_noacc_9-la1511_C_1acc_9    -1.636667e-01 -0.43742319  0.110089861
## la1511_C_noacc_9-la1511_C_5acc_9  -1.171429e-01 -0.40050778  0.166222070
## la1511_S_1acc_9-la1511_C_5acc_9    3.016667e-01  0.00673110  0.596602234
## la1511_S_5acc_9-la1511_C_5acc_9   -6.666667e-02 -0.36160223  0.228268900
## la1511_S_noacc_9-la1511_C_5acc_9  -1.171429e-01 -0.40050778  0.166222070
## m058_C_1acc_9-la1511_C_5acc_9      1.577778e-01 -0.10938124  0.424936793
## m058_C_5acc_9-la1511_C_5acc_9      3.400000e-02 -0.22724955  0.295249554
## m058_C_noacc_9-la1511_C_5acc_9     2.220000e-01 -0.03924955  0.483249554
## m058_S_1acc_9-la1511_C_5acc_9      1.150000e-01 -0.14624955  0.376249554
## m058_S_5acc_9-la1511_C_5acc_9     -4.400000e-02 -0.30524955  0.217249554
## m058_S_noacc_9-la1511_C_5acc_9     1.210000e-01 -0.14024955  0.382249554
## m248_C_1acc_9-la1511_C_5acc_9      1.790000e-01 -0.08224955  0.440249554
## m248_C_5acc_9-la1511_C_5acc_9      6.800000e-02 -0.19324955  0.329249554
## m248_C_noacc_9-la1511_C_5acc_9     8.300000e-02 -0.17824955  0.344249554
## m248_S_1acc_9-la1511_C_5acc_9      1.955556e-01 -0.07160346  0.462714571
## m248_S_5acc_9-la1511_C_5acc_9      1.800000e-02 -0.24324955  0.279249554
## m248_S_noacc_9-la1511_C_5acc_9    -9.200000e-02 -0.35324955  0.169249554
## la1511_S_1acc_9-la1511_C_noacc_9   4.188095e-01  0.12387396  0.713745091
## la1511_S_5acc_9-la1511_C_noacc_9   5.047619e-02 -0.24445938  0.345411758
## la1511_S_noacc_9-la1511_C_noacc_9 -1.942890e-16 -0.28336493  0.283364927
## m058_C_1acc_9-la1511_C_noacc_9     2.749206e-01  0.00776162  0.542079650
## m058_C_5acc_9-la1511_C_noacc_9     1.511429e-01 -0.11010670  0.412392411
## m058_C_noacc_9-la1511_C_noacc_9    3.391429e-01  0.07789330  0.600392411
## m058_S_1acc_9-la1511_C_noacc_9     2.321429e-01 -0.02910670  0.493392411
## m058_S_5acc_9-la1511_C_noacc_9     7.314286e-02 -0.18810670  0.334392411
## m058_S_noacc_9-la1511_C_noacc_9    2.381429e-01 -0.02310670  0.499392411
## m248_C_1acc_9-la1511_C_noacc_9     2.961429e-01  0.03489330  0.557392411
## m248_C_5acc_9-la1511_C_noacc_9     1.851429e-01 -0.07610670  0.446392411
## m248_C_noacc_9-la1511_C_noacc_9    2.001429e-01 -0.06110670  0.461392411
## m248_S_1acc_9-la1511_C_noacc_9     3.126984e-01  0.04553940  0.579857428
## m248_S_5acc_9-la1511_C_noacc_9     1.351429e-01 -0.12610670  0.396392411
## m248_S_noacc_9-la1511_C_noacc_9    2.514286e-02 -0.23610670  0.286392411
## la1511_S_5acc_9-la1511_S_1acc_9   -3.683333e-01 -0.67440244 -0.062264231
## la1511_S_noacc_9-la1511_S_1acc_9  -4.188095e-01 -0.71374509 -0.123873957
## m058_C_1acc_9-la1511_S_1acc_9     -1.438889e-01 -0.42329047  0.135512697
## m058_C_5acc_9-la1511_S_1acc_9     -2.676667e-01 -0.54142319  0.006089861
## m058_C_noacc_9-la1511_S_1acc_9    -7.966667e-02 -0.35342319  0.194089861
## m058_S_1acc_9-la1511_S_1acc_9     -1.866667e-01 -0.46042319  0.087089861
## m058_S_5acc_9-la1511_S_1acc_9     -3.456667e-01 -0.61942319 -0.071910139
## m058_S_noacc_9-la1511_S_1acc_9    -1.806667e-01 -0.45442319  0.093089861
## m248_C_1acc_9-la1511_S_1acc_9     -1.226667e-01 -0.39642319  0.151089861
## m248_C_5acc_9-la1511_S_1acc_9     -2.336667e-01 -0.50742319  0.040089861
## m248_C_noacc_9-la1511_S_1acc_9    -2.186667e-01 -0.49242319  0.055089861
## m248_S_1acc_9-la1511_S_1acc_9     -1.061111e-01 -0.38551270  0.173290475
## m248_S_5acc_9-la1511_S_1acc_9     -2.836667e-01 -0.55742319 -0.009910139
## m248_S_noacc_9-la1511_S_1acc_9    -3.936667e-01 -0.66742319 -0.119910139
## la1511_S_noacc_9-la1511_S_5acc_9  -5.047619e-02 -0.34541176  0.244459377
## m058_C_1acc_9-la1511_S_5acc_9      2.244444e-01 -0.05495714  0.503846030
## m058_C_5acc_9-la1511_S_5acc_9      1.006667e-01 -0.17308986  0.374423194
## m058_C_noacc_9-la1511_S_5acc_9     2.886667e-01  0.01491014  0.562423194
## m058_S_1acc_9-la1511_S_5acc_9      1.816667e-01 -0.09208986  0.455423194
## m058_S_5acc_9-la1511_S_5acc_9      2.266667e-02 -0.25108986  0.296423194
## m058_S_noacc_9-la1511_S_5acc_9     1.876667e-01 -0.08608986  0.461423194
## m248_C_1acc_9-la1511_S_5acc_9      2.456667e-01 -0.02808986  0.519423194
## m248_C_5acc_9-la1511_S_5acc_9      1.346667e-01 -0.13908986  0.408423194
## m248_C_noacc_9-la1511_S_5acc_9     1.496667e-01 -0.12408986  0.423423194
## m248_S_1acc_9-la1511_S_5acc_9      2.622222e-01 -0.01717936  0.541623808
## m248_S_5acc_9-la1511_S_5acc_9      8.466667e-02 -0.18908986  0.358423194
## m248_S_noacc_9-la1511_S_5acc_9    -2.533333e-02 -0.29908986  0.248423194
## m058_C_1acc_9-la1511_S_noacc_9     2.749206e-01  0.00776162  0.542079650
## m058_C_5acc_9-la1511_S_noacc_9     1.511429e-01 -0.11010670  0.412392411
## m058_C_noacc_9-la1511_S_noacc_9    3.391429e-01  0.07789330  0.600392411
## m058_S_1acc_9-la1511_S_noacc_9     2.321429e-01 -0.02910670  0.493392411
## m058_S_5acc_9-la1511_S_noacc_9     7.314286e-02 -0.18810670  0.334392411
## m058_S_noacc_9-la1511_S_noacc_9    2.381429e-01 -0.02310670  0.499392411
## m248_C_1acc_9-la1511_S_noacc_9     2.961429e-01  0.03489330  0.557392411
## m248_C_5acc_9-la1511_S_noacc_9     1.851429e-01 -0.07610670  0.446392411
## m248_C_noacc_9-la1511_S_noacc_9    2.001429e-01 -0.06110670  0.461392411
## m248_S_1acc_9-la1511_S_noacc_9     3.126984e-01  0.04553940  0.579857428
## m248_S_5acc_9-la1511_S_noacc_9     1.351429e-01 -0.12610670  0.396392411
## m248_S_noacc_9-la1511_S_noacc_9    2.514286e-02 -0.23610670  0.286392411
## m058_C_5acc_9-m058_C_1acc_9       -1.237778e-01 -0.36735443  0.119798878
## m058_C_noacc_9-m058_C_1acc_9       6.422222e-02 -0.17935443  0.307798878
## m058_S_1acc_9-m058_C_1acc_9       -4.277778e-02 -0.28635443  0.200798878
## m058_S_5acc_9-m058_C_1acc_9       -2.017778e-01 -0.44535443  0.041798878
## m058_S_noacc_9-m058_C_1acc_9      -3.677778e-02 -0.28035443  0.206798878
## m248_C_1acc_9-m058_C_1acc_9        2.122222e-02 -0.22235443  0.264798878
## m248_C_5acc_9-m058_C_1acc_9       -8.977778e-02 -0.33335443  0.153798878
## m248_C_noacc_9-m058_C_1acc_9      -7.477778e-02 -0.31835443  0.168798878
## m248_S_1acc_9-m058_C_1acc_9        3.777778e-02 -0.21212660  0.287682154
## m248_S_5acc_9-m058_C_1acc_9       -1.397778e-01 -0.38335443  0.103798878
## m248_S_noacc_9-m058_C_1acc_9      -2.497778e-01 -0.49335443 -0.006201122
## m058_C_noacc_9-m058_C_5acc_9       1.880000e-01 -0.04908011  0.425080107
## m058_S_1acc_9-m058_C_5acc_9        8.100000e-02 -0.15608011  0.318080107
## m058_S_5acc_9-m058_C_5acc_9       -7.800000e-02 -0.31508011  0.159080107
## m058_S_noacc_9-m058_C_5acc_9       8.700000e-02 -0.15008011  0.324080107
## m248_C_1acc_9-m058_C_5acc_9        1.450000e-01 -0.09208011  0.382080107
## m248_C_5acc_9-m058_C_5acc_9        3.400000e-02 -0.20308011  0.271080107
## m248_C_noacc_9-m058_C_5acc_9       4.900000e-02 -0.18808011  0.286080107
## m248_S_1acc_9-m058_C_5acc_9        1.615556e-01 -0.08202110  0.405132211
## m248_S_5acc_9-m058_C_5acc_9       -1.600000e-02 -0.25308011  0.221080107
## m248_S_noacc_9-m058_C_5acc_9      -1.260000e-01 -0.36308011  0.111080107
## m058_S_1acc_9-m058_C_noacc_9      -1.070000e-01 -0.34408011  0.130080107
## m058_S_5acc_9-m058_C_noacc_9      -2.660000e-01 -0.50308011 -0.028919893
## m058_S_noacc_9-m058_C_noacc_9     -1.010000e-01 -0.33808011  0.136080107
## m248_C_1acc_9-m058_C_noacc_9      -4.300000e-02 -0.28008011  0.194080107
## m248_C_5acc_9-m058_C_noacc_9      -1.540000e-01 -0.39108011  0.083080107
## m248_C_noacc_9-m058_C_noacc_9     -1.390000e-01 -0.37608011  0.098080107
## m248_S_1acc_9-m058_C_noacc_9      -2.644444e-02 -0.27002110  0.217132211
## m248_S_5acc_9-m058_C_noacc_9      -2.040000e-01 -0.44108011  0.033080107
## m248_S_noacc_9-m058_C_noacc_9     -3.140000e-01 -0.55108011 -0.076919893
## m058_S_5acc_9-m058_S_1acc_9       -1.590000e-01 -0.39608011  0.078080107
## m058_S_noacc_9-m058_S_1acc_9       6.000000e-03 -0.23108011  0.243080107
## m248_C_1acc_9-m058_S_1acc_9        6.400000e-02 -0.17308011  0.301080107
## m248_C_5acc_9-m058_S_1acc_9       -4.700000e-02 -0.28408011  0.190080107
## m248_C_noacc_9-m058_S_1acc_9      -3.200000e-02 -0.26908011  0.205080107
## m248_S_1acc_9-m058_S_1acc_9        8.055556e-02 -0.16302110  0.324132211
## m248_S_5acc_9-m058_S_1acc_9       -9.700000e-02 -0.33408011  0.140080107
## m248_S_noacc_9-m058_S_1acc_9      -2.070000e-01 -0.44408011  0.030080107
## m058_S_noacc_9-m058_S_5acc_9       1.650000e-01 -0.07208011  0.402080107
## m248_C_1acc_9-m058_S_5acc_9        2.230000e-01 -0.01408011  0.460080107
## m248_C_5acc_9-m058_S_5acc_9        1.120000e-01 -0.12508011  0.349080107
## m248_C_noacc_9-m058_S_5acc_9       1.270000e-01 -0.11008011  0.364080107
## m248_S_1acc_9-m058_S_5acc_9        2.395556e-01 -0.00402110  0.483132211
## m248_S_5acc_9-m058_S_5acc_9        6.200000e-02 -0.17508011  0.299080107
## m248_S_noacc_9-m058_S_5acc_9      -4.800000e-02 -0.28508011  0.189080107
## m248_C_1acc_9-m058_S_noacc_9       5.800000e-02 -0.17908011  0.295080107
## m248_C_5acc_9-m058_S_noacc_9      -5.300000e-02 -0.29008011  0.184080107
## m248_C_noacc_9-m058_S_noacc_9     -3.800000e-02 -0.27508011  0.199080107
## m248_S_1acc_9-m058_S_noacc_9       7.455556e-02 -0.16902110  0.318132211
## m248_S_5acc_9-m058_S_noacc_9      -1.030000e-01 -0.34008011  0.134080107
## m248_S_noacc_9-m058_S_noacc_9     -2.130000e-01 -0.45008011  0.024080107
## m248_C_5acc_9-m248_C_1acc_9       -1.110000e-01 -0.34808011  0.126080107
## m248_C_noacc_9-m248_C_1acc_9      -9.600000e-02 -0.33308011  0.141080107
## m248_S_1acc_9-m248_C_1acc_9        1.655556e-02 -0.22702110  0.260132211
## m248_S_5acc_9-m248_C_1acc_9       -1.610000e-01 -0.39808011  0.076080107
## m248_S_noacc_9-m248_C_1acc_9      -2.710000e-01 -0.50808011 -0.033919893
## m248_C_noacc_9-m248_C_5acc_9       1.500000e-02 -0.22208011  0.252080107
## m248_S_1acc_9-m248_C_5acc_9        1.275556e-01 -0.11602110  0.371132211
## m248_S_5acc_9-m248_C_5acc_9       -5.000000e-02 -0.28708011  0.187080107
## m248_S_noacc_9-m248_C_5acc_9      -1.600000e-01 -0.39708011  0.077080107
## m248_S_1acc_9-m248_C_noacc_9       1.125556e-01 -0.13102110  0.356132211
## m248_S_5acc_9-m248_C_noacc_9      -6.500000e-02 -0.30208011  0.172080107
## m248_S_noacc_9-m248_C_noacc_9     -1.750000e-01 -0.41208011  0.062080107
## m248_S_5acc_9-m248_S_1acc_9       -1.775556e-01 -0.42113221  0.066021100
## m248_S_noacc_9-m248_S_1acc_9      -2.875556e-01 -0.53113221 -0.043978900
## m248_S_noacc_9-m248_S_5acc_9      -1.100000e-01 -0.34708011  0.127080107
##                                       p adj
## la1511_C_5acc_9-la1511_C_1acc_9   0.9999909
## la1511_C_noacc_9-la1511_C_1acc_9  0.6985742
## la1511_S_1acc_9-la1511_C_1acc_9   0.4098643
## la1511_S_5acc_9-la1511_C_1acc_9   0.9785602
## la1511_S_noacc_9-la1511_C_1acc_9  0.6985742
## m058_C_1acc_9-la1511_C_1acc_9     0.9997501
## m058_C_5acc_9-la1511_C_1acc_9     1.0000000
## m058_C_noacc_9-la1511_C_1acc_9    0.8857124
## m058_S_1acc_9-la1511_C_1acc_9     1.0000000
## m058_S_5acc_9-la1511_C_1acc_9     0.9891684
## m058_S_noacc_9-la1511_C_1acc_9    0.9999999
## m248_C_1acc_9-la1511_C_1acc_9     0.9951969
## m248_C_5acc_9-la1511_C_1acc_9     1.0000000
## m248_C_noacc_9-la1511_C_1acc_9    1.0000000
## m248_S_1acc_9-la1511_C_1acc_9     0.9822471
## m248_S_5acc_9-la1511_C_1acc_9     0.9999996
## m248_S_noacc_9-la1511_C_1acc_9    0.7964949
## la1511_C_noacc_9-la1511_C_5acc_9  0.9914062
## la1511_S_1acc_9-la1511_C_5acc_9   0.0390776
## la1511_S_5acc_9-la1511_C_5acc_9   0.9999968
## la1511_S_noacc_9-la1511_C_5acc_9  0.9914062
## m058_C_1acc_9-la1511_C_5acc_9     0.8116025
## m058_C_5acc_9-la1511_C_5acc_9     1.0000000
## m058_C_noacc_9-la1511_C_5acc_9    0.2048806
## m058_S_1acc_9-la1511_C_5acc_9     0.9834952
## m058_S_5acc_9-la1511_C_5acc_9     1.0000000
## m058_S_noacc_9-la1511_C_5acc_9    0.9728709
## m248_C_1acc_9-la1511_C_5acc_9     0.5821257
## m248_C_5acc_9-la1511_C_5acc_9     0.9999754
## m248_C_noacc_9-la1511_C_5acc_9    0.9996279
## m248_S_1acc_9-la1511_C_5acc_9     0.4589881
## m248_S_5acc_9-la1511_C_5acc_9     1.0000000
## m248_S_noacc_9-la1511_C_5acc_9    0.9986378
## la1511_S_1acc_9-la1511_C_noacc_9  0.0001927
## la1511_S_5acc_9-la1511_C_noacc_9  1.0000000
## la1511_S_noacc_9-la1511_C_noacc_9 1.0000000
## m058_C_1acc_9-la1511_C_noacc_9    0.0364859
## m058_C_5acc_9-la1511_C_noacc_9    0.8352781
## m058_C_noacc_9-la1511_C_noacc_9   0.0011743
## m058_S_1acc_9-la1511_C_noacc_9    0.1477962
## m058_S_5acc_9-la1511_C_noacc_9    0.9999317
## m058_S_noacc_9-la1511_C_noacc_9   0.1202570
## m248_C_1acc_9-la1511_C_noacc_9    0.0106540
## m248_C_5acc_9-la1511_C_noacc_9    0.5197857
## m248_C_noacc_9-la1511_C_noacc_9   0.3744177
## m248_S_1acc_9-la1511_C_noacc_9    0.0066725
## m248_S_5acc_9-la1511_C_noacc_9    0.9280793
## m248_S_noacc_9-la1511_C_noacc_9   1.0000000
## la1511_S_5acc_9-la1511_S_1acc_9   0.0043332
## la1511_S_noacc_9-la1511_S_1acc_9  0.0001927
## m058_C_1acc_9-la1511_S_1acc_9     0.9306540
## m058_C_5acc_9-la1511_S_1acc_9     0.0630952
## m058_C_noacc_9-la1511_S_1acc_9    0.9998841
## m058_S_1acc_9-la1511_S_1acc_9     0.5908620
## m058_S_5acc_9-la1511_S_1acc_9     0.0019359
## m058_S_noacc_9-la1511_S_1acc_9    0.6483405
## m248_C_1acc_9-la1511_S_1acc_9     0.9802994
## m248_C_5acc_9-la1511_S_1acc_9     0.1986936
## m248_C_noacc_9-la1511_S_1acc_9    0.3009750
## m248_S_1acc_9-la1511_S_1acc_9     0.9966593
## m248_S_5acc_9-la1511_S_1acc_9     0.0337000
## m248_S_noacc_9-la1511_S_1acc_9    0.0001459
## la1511_S_noacc_9-la1511_S_5acc_9  1.0000000
## m058_C_1acc_9-la1511_S_5acc_9     0.2914623
## m058_C_5acc_9-la1511_S_5acc_9     0.9977088
## m058_C_noacc_9-la1511_S_5acc_9    0.0274191
## m058_S_1acc_9-la1511_S_5acc_9     0.6388616
## m058_S_5acc_9-la1511_S_5acc_9     1.0000000
## m058_S_noacc_9-la1511_S_5acc_9    0.5811835
## m248_C_1acc_9-la1511_S_5acc_9     0.1367151
## m248_C_5acc_9-la1511_S_5acc_9     0.9529848
## m248_C_noacc_9-la1511_S_5acc_9    0.8894046
## m248_S_1acc_9-la1511_S_5acc_9     0.0932971
## m248_S_5acc_9-la1511_S_5acc_9     0.9997383
## m248_S_noacc_9-la1511_S_5acc_9    1.0000000
## m058_C_1acc_9-la1511_S_noacc_9    0.0364859
## m058_C_5acc_9-la1511_S_noacc_9    0.8352781
## m058_C_noacc_9-la1511_S_noacc_9   0.0011743
## m058_S_1acc_9-la1511_S_noacc_9    0.1477962
## m058_S_5acc_9-la1511_S_noacc_9    0.9999317
## m058_S_noacc_9-la1511_S_noacc_9   0.1202570
## m248_C_1acc_9-la1511_S_noacc_9    0.0106540
## m248_C_5acc_9-la1511_S_noacc_9    0.5197857
## m248_C_noacc_9-la1511_S_noacc_9   0.3744177
## m248_S_1acc_9-la1511_S_noacc_9    0.0066725
## m248_S_5acc_9-la1511_S_noacc_9    0.9280793
## m248_S_noacc_9-la1511_S_noacc_9   1.0000000
## m058_C_5acc_9-m058_C_1acc_9       0.9379009
## m058_C_noacc_9-m058_C_1acc_9      0.9999705
## m058_S_1acc_9-m058_C_1acc_9       0.9999999
## m058_S_5acc_9-m058_C_1acc_9       0.2422270
## m058_S_noacc_9-m058_C_1acc_9      1.0000000
## m248_C_1acc_9-m058_C_1acc_9       1.0000000
## m248_C_5acc_9-m058_C_1acc_9       0.9976448
## m248_C_noacc_9-m058_C_1acc_9      0.9997626
## m248_S_1acc_9-m058_C_1acc_9       1.0000000
## m248_S_5acc_9-m058_C_1acc_9       0.8440280
## m248_S_noacc_9-m058_C_1acc_9      0.0379618
## m058_C_noacc_9-m058_C_5acc_9      0.3133462
## m058_S_1acc_9-m058_C_5acc_9       0.9990618
## m058_S_5acc_9-m058_C_5acc_9       0.9994167
## m058_S_noacc_9-m058_C_5acc_9      0.9977641
## m248_C_1acc_9-m058_C_5acc_9       0.7664347
## m248_C_5acc_9-m058_C_5acc_9       1.0000000
## m248_C_noacc_9-m058_C_5acc_9      0.9999992
## m248_S_1acc_9-m058_C_5acc_9       0.6397538
## m248_S_5acc_9-m058_C_5acc_9       1.0000000
## m248_S_noacc_9-m058_C_5acc_9      0.9108090
## m058_S_1acc_9-m058_C_noacc_9      0.9788565
## m058_S_5acc_9-m058_C_noacc_9      0.0122972
## m058_S_noacc_9-m058_C_noacc_9     0.9881931
## m248_C_1acc_9-m058_C_noacc_9      0.9999999
## m248_C_5acc_9-m058_C_noacc_9      0.6749696
## m248_C_noacc_9-m058_C_noacc_9     0.8202045
## m248_S_1acc_9-m058_C_noacc_9      1.0000000
## m248_S_5acc_9-m058_C_noacc_9      0.1877659
## m248_S_noacc_9-m058_C_noacc_9     0.0008043
## m058_S_5acc_9-m058_S_1acc_9       0.6204288
## m058_S_noacc_9-m058_S_1acc_9      1.0000000
## m248_C_1acc_9-m058_S_1acc_9       0.9999589
## m248_C_5acc_9-m058_S_1acc_9       0.9999996
## m248_C_noacc_9-m058_S_1acc_9      1.0000000
## m248_S_1acc_9-m058_S_1acc_9       0.9993768
## m248_S_5acc_9-m058_S_1acc_9       0.9923126
## m248_S_noacc_9-m058_S_1acc_9      0.1688980
## m058_S_noacc_9-m058_S_5acc_9      0.5534666
## m248_C_1acc_9-m058_S_5acc_9       0.0914260
## m248_C_5acc_9-m058_S_5acc_9       0.9673469
## m248_C_noacc_9-m058_S_5acc_9      0.9051834
## m248_S_1acc_9-m058_S_5acc_9       0.0594651
## m248_S_5acc_9-m058_S_5acc_9       0.9999737
## m248_S_noacc_9-m058_S_5acc_9      0.9999994
## m248_C_1acc_9-m058_S_noacc_9      0.9999899
## m248_C_5acc_9-m058_S_noacc_9      0.9999973
## m248_C_noacc_9-m058_S_noacc_9     1.0000000
## m248_S_1acc_9-m058_S_noacc_9      0.9997718
## m248_S_5acc_9-m058_S_noacc_9      0.9855495
## m248_S_noacc_9-m058_S_noacc_9     0.1354505
## m248_C_5acc_9-m248_C_1acc_9       0.9699609
## m248_C_noacc_9-m248_C_1acc_9      0.9931321
## m248_S_1acc_9-m248_C_1acc_9       1.0000000
## m248_S_5acc_9-m248_C_1acc_9       0.5982047
## m248_S_noacc_9-m248_C_1acc_9      0.0094582
## m248_C_noacc_9-m248_C_5acc_9      1.0000000
## m248_S_1acc_9-m248_C_5acc_9       0.9206091
## m248_S_5acc_9-m248_C_5acc_9       0.9999989
## m248_S_noacc_9-m248_C_5acc_9      0.6093366
## m248_S_1acc_9-m248_C_noacc_9      0.9734568
## m248_S_5acc_9-m248_C_noacc_9      0.9999489
## m248_S_noacc_9-m248_C_noacc_9     0.4432357
## m248_S_5acc_9-m248_S_1acc_9       0.4667917
## m248_S_noacc_9-m248_S_1acc_9      0.0058541
## m248_S_noacc_9-m248_S_5acc_9      0.9724129
P6 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P6)
stat.test
##  la1511_C_5acc_9 la1511_C_noacc_9  la1511_S_1acc_9  la1511_S_5acc_9 
##            "abc"              "a"              "d"             "ab" 
## la1511_S_noacc_9    m058_C_1acc_9    m058_C_5acc_9   m058_C_noacc_9 
##              "a"            "bcd"           "abcd"             "cd" 
##    m058_S_1acc_9    m058_S_5acc_9   m058_S_noacc_9    m248_C_1acc_9 
##           "abcd"             "ab"           "abcd"            "bcd" 
##    m248_C_5acc_9   m248_C_noacc_9    m248_S_1acc_9    m248_S_5acc_9 
##           "abcd"           "abcd"            "bcd"            "abc" 
##   m248_S_noacc_9  la1511_C_1acc_9 
##              "a"           "abcd"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ACC_pareto_location2$Condition.all <- factor(ACC_pareto_location2$Condition.all, levels = c("C_noacc", "C_1acc","C_5acc",  "S_noacc","S_1acc","S_5acc"))

ACC_pareto_location_graph <- ggplot(data = ACC_pareto_location2, mapping = aes(x = All.ID, y = pareto.front.scaling.location
, colour = Condition.all)) 
ACC_pareto_location_graph  <- ACC_pareto_location_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ACC_pareto_location_graph  <- ACC_pareto_location_graph  + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ACC_pareto_location_graph  <- ACC_pareto_location_graph  + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ACC_pareto_location_graph  <- ACC_pareto_location_graph  + ylab("Pareto front location") + xlab("") #+ ggtitle("")
ACC_pareto_location_graph  <- ACC_pareto_location_graph  + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
ACC_pareto_location_graph  <- ACC_pareto_location_graph  + stat_pvalue_manual(test, label = "Tukey", y.position = 1.5)
ACC_pareto_location_graph 

ACC_pareto_location_graph <- ggplot(data=ACC_pareto_location2, aes(x= Condition.all, y=pareto.front.scaling.location, color = Condition.all)) 
ACC_pareto_location_graph <- ACC_pareto_location_graph +  geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ACC_pareto_location_graph <- ACC_pareto_location_graph + facet_grid(~ Accessions )

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

aov(pareto.front.scaling.distance ~ All.ID, data = ACC_pareto_location2)
## Call:
##    aov(formula = pareto.front.scaling.distance ~ All.ID, data = ACC_pareto_location2)
## 
## Terms:
##                     All.ID  Residuals
## Sum of Squares  0.07818364 0.30242277
## Deg. of Freedom         17        139
## 
## Residual standard error: 0.04664444
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(pareto.front.scaling.distance ~ All.ID, data = ACC_pareto_location2))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = pareto.front.scaling.distance ~ All.ID, data = ACC_pareto_location2)
## 
## $All.ID
##                                            diff          lwr        upr
## la1511_C_5acc_9-la1511_C_1acc_9   -0.0438510952 -0.136121096 0.04841891
## la1511_C_noacc_9-la1511_C_1acc_9  -0.0343358095 -0.126605811 0.05793419
## la1511_S_1acc_9-la1511_C_1acc_9   -0.0038185000 -0.099571605 0.09193461
## la1511_S_5acc_9-la1511_C_1acc_9    0.0167063333 -0.079046772 0.11245944
## la1511_S_noacc_9-la1511_C_1acc_9  -0.0408703810 -0.133140382 0.05139962
## m058_C_1acc_9-la1511_C_1acc_9     -0.0011174444 -0.088527671 0.08629278
## m058_C_5acc_9-la1511_C_1acc_9     -0.0126550667 -0.098299248 0.07298911
## m058_C_noacc_9-la1511_C_1acc_9    -0.0352793667 -0.120923548 0.05036481
## m058_S_1acc_9-la1511_C_1acc_9     -0.0142220667 -0.099866248 0.07142211
## m058_S_5acc_9-la1511_C_1acc_9     -0.0229199667 -0.108564148 0.06272421
## m058_S_noacc_9-la1511_C_1acc_9     0.0170643333 -0.068579848 0.10270851
## m248_C_1acc_9-la1511_C_1acc_9     -0.0101727667 -0.095816948 0.07547141
## m248_C_5acc_9-la1511_C_1acc_9      0.0248393333 -0.060804848 0.11048351
## m248_C_noacc_9-la1511_C_1acc_9     0.0179967333 -0.067647448 0.10364091
## m248_S_1acc_9-la1511_C_1acc_9      0.0025175556 -0.084892671 0.08992778
## m248_S_5acc_9-la1511_C_1acc_9      0.0114115333 -0.074232648 0.09705571
## m248_S_noacc_9-la1511_C_1acc_9     0.0313379333 -0.054306248 0.11698211
## la1511_C_noacc_9-la1511_C_5acc_9   0.0095152857 -0.079134864 0.09816544
## la1511_S_1acc_9-la1511_C_5acc_9    0.0400325952 -0.052237406 0.13230260
## la1511_S_5acc_9-la1511_C_5acc_9    0.0605574286 -0.031712572 0.15282743
## la1511_S_noacc_9-la1511_C_5acc_9   0.0029807143 -0.085669435 0.09163086
## m058_C_1acc_9-la1511_C_5acc_9      0.0427336508 -0.040846512 0.12631381
## m058_C_5acc_9-la1511_C_5acc_9      0.0311960286 -0.050535371 0.11292743
## m058_C_noacc_9-la1511_C_5acc_9     0.0085717286 -0.073159671 0.09030313
## m058_S_1acc_9-la1511_C_5acc_9      0.0296290286 -0.052102371 0.11136043
## m058_S_5acc_9-la1511_C_5acc_9      0.0209311286 -0.060800271 0.10266253
## m058_S_noacc_9-la1511_C_5acc_9     0.0609154286 -0.020815971 0.14264683
## m248_C_1acc_9-la1511_C_5acc_9      0.0336783286 -0.048053071 0.11540973
## m248_C_5acc_9-la1511_C_5acc_9      0.0686904286 -0.013040971 0.15042183
## m248_C_noacc_9-la1511_C_5acc_9     0.0618478286 -0.019883571 0.14357923
## m248_S_1acc_9-la1511_C_5acc_9      0.0463686508 -0.037211512 0.12994881
## m248_S_5acc_9-la1511_C_5acc_9      0.0552626286 -0.026468771 0.13699403
## m248_S_noacc_9-la1511_C_5acc_9     0.0751890286 -0.006542371 0.15692043
## la1511_S_1acc_9-la1511_C_noacc_9   0.0305173095 -0.061752692 0.12278731
## la1511_S_5acc_9-la1511_C_noacc_9   0.0510421429 -0.041227858 0.14331214
## la1511_S_noacc_9-la1511_C_noacc_9 -0.0065345714 -0.095184721 0.08211558
## m058_C_1acc_9-la1511_C_noacc_9     0.0332183651 -0.050361797 0.11679853
## m058_C_5acc_9-la1511_C_noacc_9     0.0216807429 -0.060050657 0.10341214
## m058_C_noacc_9-la1511_C_noacc_9   -0.0009435571 -0.082674957 0.08078784
## m058_S_1acc_9-la1511_C_noacc_9     0.0201137429 -0.061617657 0.10184514
## m058_S_5acc_9-la1511_C_noacc_9     0.0114158429 -0.070315557 0.09314724
## m058_S_noacc_9-la1511_C_noacc_9    0.0514001429 -0.030331257 0.13313154
## m248_C_1acc_9-la1511_C_noacc_9     0.0241630429 -0.057568357 0.10589444
## m248_C_5acc_9-la1511_C_noacc_9     0.0591751429 -0.022556257 0.14090654
## m248_C_noacc_9-la1511_C_noacc_9    0.0523325429 -0.029398857 0.13406394
## m248_S_1acc_9-la1511_C_noacc_9     0.0368533651 -0.046726797 0.12043353
## m248_S_5acc_9-la1511_C_noacc_9     0.0457473429 -0.035984057 0.12747874
## m248_S_noacc_9-la1511_C_noacc_9    0.0656737429 -0.016057657 0.14740514
## la1511_S_5acc_9-la1511_S_1acc_9    0.0205248333 -0.075228272 0.11627794
## la1511_S_noacc_9-la1511_S_1acc_9  -0.0370518810 -0.129321882 0.05521812
## m058_C_1acc_9-la1511_S_1acc_9      0.0027010556 -0.084709171 0.09011128
## m058_C_5acc_9-la1511_S_1acc_9     -0.0088365667 -0.094480748 0.07680761
## m058_C_noacc_9-la1511_S_1acc_9    -0.0314608667 -0.117105048 0.05418331
## m058_S_1acc_9-la1511_S_1acc_9     -0.0104035667 -0.096047748 0.07524061
## m058_S_5acc_9-la1511_S_1acc_9     -0.0191014667 -0.104745648 0.06654271
## m058_S_noacc_9-la1511_S_1acc_9     0.0208828333 -0.064761348 0.10652701
## m248_C_1acc_9-la1511_S_1acc_9     -0.0063542667 -0.091998448 0.07928991
## m248_C_5acc_9-la1511_S_1acc_9      0.0286578333 -0.056986348 0.11430201
## m248_C_noacc_9-la1511_S_1acc_9     0.0218152333 -0.063828948 0.10745941
## m248_S_1acc_9-la1511_S_1acc_9      0.0063360556 -0.081074171 0.09374628
## m248_S_5acc_9-la1511_S_1acc_9      0.0152300333 -0.070414148 0.10087421
## m248_S_noacc_9-la1511_S_1acc_9     0.0351564333 -0.050487748 0.12080061
## la1511_S_noacc_9-la1511_S_5acc_9  -0.0575767143 -0.149846715 0.03469329
## m058_C_1acc_9-la1511_S_5acc_9     -0.0178237778 -0.105234004 0.06958645
## m058_C_5acc_9-la1511_S_5acc_9     -0.0293614000 -0.115005581 0.05628278
## m058_C_noacc_9-la1511_S_5acc_9    -0.0519857000 -0.137629881 0.03365848
## m058_S_1acc_9-la1511_S_5acc_9     -0.0309284000 -0.116572581 0.05471578
## m058_S_5acc_9-la1511_S_5acc_9     -0.0396263000 -0.125270481 0.04601788
## m058_S_noacc_9-la1511_S_5acc_9     0.0003580000 -0.085286181 0.08600218
## m248_C_1acc_9-la1511_S_5acc_9     -0.0268791000 -0.112523281 0.05876508
## m248_C_5acc_9-la1511_S_5acc_9      0.0081330000 -0.077511181 0.09377718
## m248_C_noacc_9-la1511_S_5acc_9     0.0012904000 -0.084353781 0.08693458
## m248_S_1acc_9-la1511_S_5acc_9     -0.0141887778 -0.101599004 0.07322145
## m248_S_5acc_9-la1511_S_5acc_9     -0.0052948000 -0.090938981 0.08034938
## m248_S_noacc_9-la1511_S_5acc_9     0.0146316000 -0.071012581 0.10027578
## m058_C_1acc_9-la1511_S_noacc_9     0.0397529365 -0.043827226 0.12333310
## m058_C_5acc_9-la1511_S_noacc_9     0.0282153143 -0.053516085 0.10994671
## m058_C_noacc_9-la1511_S_noacc_9    0.0055910143 -0.076140385 0.08732241
## m058_S_1acc_9-la1511_S_noacc_9     0.0266483143 -0.055083085 0.10837971
## m058_S_5acc_9-la1511_S_noacc_9     0.0179504143 -0.063780985 0.09968181
## m058_S_noacc_9-la1511_S_noacc_9    0.0579347143 -0.023796685 0.13966611
## m248_C_1acc_9-la1511_S_noacc_9     0.0306976143 -0.051033785 0.11242901
## m248_C_5acc_9-la1511_S_noacc_9     0.0657097143 -0.016021685 0.14744111
## m248_C_noacc_9-la1511_S_noacc_9    0.0588671143 -0.022864285 0.14059851
## m248_S_1acc_9-la1511_S_noacc_9     0.0433879365 -0.040192226 0.12696810
## m248_S_5acc_9-la1511_S_noacc_9     0.0522819143 -0.029449485 0.13401331
## m248_S_noacc_9-la1511_S_noacc_9    0.0722083143 -0.009523085 0.15393971
## m058_C_5acc_9-m058_C_1acc_9       -0.0115376222 -0.087740091 0.06466485
## m058_C_noacc_9-m058_C_1acc_9      -0.0341619222 -0.110364391 0.04204055
## m058_S_1acc_9-m058_C_1acc_9       -0.0131046222 -0.089307091 0.06309785
## m058_S_5acc_9-m058_C_1acc_9       -0.0218025222 -0.098004991 0.05439995
## m058_S_noacc_9-m058_C_1acc_9       0.0181817778 -0.058020691 0.09438425
## m248_C_1acc_9-m058_C_1acc_9       -0.0090553222 -0.085257791 0.06714715
## m248_C_5acc_9-m058_C_1acc_9        0.0259567778 -0.050245691 0.10215925
## m248_C_noacc_9-m058_C_1acc_9       0.0191141778 -0.057088291 0.09531665
## m248_S_1acc_9-m058_C_1acc_9        0.0036350000 -0.074547083 0.08181708
## m248_S_5acc_9-m058_C_1acc_9        0.0125289778 -0.063673491 0.08873145
## m248_S_noacc_9-m058_C_1acc_9       0.0324553778 -0.043747091 0.10865785
## m058_C_noacc_9-m058_C_5acc_9      -0.0226243000 -0.096794336 0.05154574
## m058_S_1acc_9-m058_C_5acc_9       -0.0015670000 -0.075737036 0.07260304
## m058_S_5acc_9-m058_C_5acc_9       -0.0102649000 -0.084434936 0.06390514
## m058_S_noacc_9-m058_C_5acc_9       0.0297194000 -0.044450636 0.10388944
## m248_C_1acc_9-m058_C_5acc_9        0.0024823000 -0.071687736 0.07665234
## m248_C_5acc_9-m058_C_5acc_9        0.0374944000 -0.036675636 0.11166444
## m248_C_noacc_9-m058_C_5acc_9       0.0306518000 -0.043518236 0.10482184
## m248_S_1acc_9-m058_C_5acc_9        0.0151726222 -0.061029846 0.09137509
## m248_S_5acc_9-m058_C_5acc_9        0.0240666000 -0.050103436 0.09823664
## m248_S_noacc_9-m058_C_5acc_9       0.0439930000 -0.030177036 0.11816304
## m058_S_1acc_9-m058_C_noacc_9       0.0210573000 -0.053112736 0.09522734
## m058_S_5acc_9-m058_C_noacc_9       0.0123594000 -0.061810636 0.08652944
## m058_S_noacc_9-m058_C_noacc_9      0.0523437000 -0.021826336 0.12651374
## m248_C_1acc_9-m058_C_noacc_9       0.0251066000 -0.049063436 0.09927664
## m248_C_5acc_9-m058_C_noacc_9       0.0601187000 -0.014051336 0.13428874
## m248_C_noacc_9-m058_C_noacc_9      0.0532761000 -0.020893936 0.12744614
## m248_S_1acc_9-m058_C_noacc_9       0.0377969222 -0.038405546 0.11399939
## m248_S_5acc_9-m058_C_noacc_9       0.0466909000 -0.027479136 0.12086094
## m248_S_noacc_9-m058_C_noacc_9      0.0666173000 -0.007552736 0.14078734
## m058_S_5acc_9-m058_S_1acc_9       -0.0086979000 -0.082867936 0.06547214
## m058_S_noacc_9-m058_S_1acc_9       0.0312864000 -0.042883636 0.10545644
## m248_C_1acc_9-m058_S_1acc_9        0.0040493000 -0.070120736 0.07821934
## m248_C_5acc_9-m058_S_1acc_9        0.0390614000 -0.035108636 0.11323144
## m248_C_noacc_9-m058_S_1acc_9       0.0322188000 -0.041951236 0.10638884
## m248_S_1acc_9-m058_S_1acc_9        0.0167396222 -0.059462846 0.09294209
## m248_S_5acc_9-m058_S_1acc_9        0.0256336000 -0.048536436 0.09980364
## m248_S_noacc_9-m058_S_1acc_9       0.0455600000 -0.028610036 0.11973004
## m058_S_noacc_9-m058_S_5acc_9       0.0399843000 -0.034185736 0.11415434
## m248_C_1acc_9-m058_S_5acc_9        0.0127472000 -0.061422836 0.08691724
## m248_C_5acc_9-m058_S_5acc_9        0.0477593000 -0.026410736 0.12192934
## m248_C_noacc_9-m058_S_5acc_9       0.0409167000 -0.033253336 0.11508674
## m248_S_1acc_9-m058_S_5acc_9        0.0254375222 -0.050764946 0.10163999
## m248_S_5acc_9-m058_S_5acc_9        0.0343315000 -0.039838536 0.10850154
## m248_S_noacc_9-m058_S_5acc_9       0.0542579000 -0.019912136 0.12842794
## m248_C_1acc_9-m058_S_noacc_9      -0.0272371000 -0.101407136 0.04693294
## m248_C_5acc_9-m058_S_noacc_9       0.0077750000 -0.066395036 0.08194504
## m248_C_noacc_9-m058_S_noacc_9      0.0009324000 -0.073237636 0.07510244
## m248_S_1acc_9-m058_S_noacc_9      -0.0145467778 -0.090749246 0.06165569
## m248_S_5acc_9-m058_S_noacc_9      -0.0056528000 -0.079822836 0.06851724
## m248_S_noacc_9-m058_S_noacc_9      0.0142736000 -0.059896436 0.08844364
## m248_C_5acc_9-m248_C_1acc_9        0.0350121000 -0.039157936 0.10918214
## m248_C_noacc_9-m248_C_1acc_9       0.0281695000 -0.046000536 0.10233954
## m248_S_1acc_9-m248_C_1acc_9        0.0126903222 -0.063512146 0.08889279
## m248_S_5acc_9-m248_C_1acc_9        0.0215843000 -0.052585736 0.09575434
## m248_S_noacc_9-m248_C_1acc_9       0.0415107000 -0.032659336 0.11568074
## m248_C_noacc_9-m248_C_5acc_9      -0.0068426000 -0.081012636 0.06732744
## m248_S_1acc_9-m248_C_5acc_9       -0.0223217778 -0.098524246 0.05388069
## m248_S_5acc_9-m248_C_5acc_9       -0.0134278000 -0.087597836 0.06074224
## m248_S_noacc_9-m248_C_5acc_9       0.0064986000 -0.067671436 0.08066864
## m248_S_1acc_9-m248_C_noacc_9      -0.0154791778 -0.091681646 0.06072329
## m248_S_5acc_9-m248_C_noacc_9      -0.0065852000 -0.080755236 0.06758484
## m248_S_noacc_9-m248_C_noacc_9      0.0133412000 -0.060828836 0.08751124
## m248_S_5acc_9-m248_S_1acc_9        0.0088939778 -0.067308491 0.08509645
## m248_S_noacc_9-m248_S_1acc_9       0.0288203778 -0.047382091 0.10502285
## m248_S_noacc_9-m248_S_5acc_9       0.0199264000 -0.054243636 0.09409644
##                                       p adj
## la1511_C_5acc_9-la1511_C_1acc_9   0.9654970
## la1511_C_noacc_9-la1511_C_1acc_9  0.9973642
## la1511_S_1acc_9-la1511_C_1acc_9   1.0000000
## la1511_S_5acc_9-la1511_C_1acc_9   0.9999999
## la1511_S_noacc_9-la1511_C_1acc_9  0.9824319
## m058_C_1acc_9-la1511_C_1acc_9     1.0000000
## m058_C_5acc_9-la1511_C_1acc_9     1.0000000
## m058_C_noacc_9-la1511_C_1acc_9    0.9917287
## m058_S_1acc_9-la1511_C_1acc_9     1.0000000
## m058_S_5acc_9-la1511_C_1acc_9     0.9999636
## m058_S_noacc_9-la1511_C_1acc_9    0.9999995
## m248_C_1acc_9-la1511_C_1acc_9     1.0000000
## m248_C_5acc_9-la1511_C_1acc_9     0.9998893
## m248_C_noacc_9-la1511_C_1acc_9    0.9999989
## m248_S_1acc_9-la1511_C_1acc_9     1.0000000
## m248_S_5acc_9-la1511_C_1acc_9     1.0000000
## m248_S_noacc_9-la1511_C_1acc_9    0.9978393
## la1511_C_noacc_9-la1511_C_5acc_9  1.0000000
## la1511_S_1acc_9-la1511_C_5acc_9   0.9857481
## la1511_S_5acc_9-la1511_C_5acc_9   0.6577500
## la1511_S_noacc_9-la1511_C_5acc_9  1.0000000
## m058_C_1acc_9-la1511_C_5acc_9     0.9346536
## m058_C_5acc_9-la1511_C_5acc_9     0.9964606
## m058_C_noacc_9-la1511_C_5acc_9    1.0000000
## m058_S_1acc_9-la1511_C_5acc_9     0.9980662
## m058_S_5acc_9-la1511_C_5acc_9     0.9999805
## m058_S_noacc_9-la1511_C_5acc_9    0.4251604
## m248_C_1acc_9-la1511_C_5acc_9     0.9917002
## m248_C_5acc_9-la1511_C_5acc_9     0.2206490
## m248_C_noacc_9-la1511_C_5acc_9    0.3969733
## m248_S_1acc_9-la1511_C_5acc_9     0.8768865
## m248_S_5acc_9-la1511_C_5acc_9     0.6059835
## m248_S_noacc_9-la1511_C_5acc_9    0.1112620
## la1511_S_1acc_9-la1511_C_noacc_9  0.9993763
## la1511_S_5acc_9-la1511_C_noacc_9  0.8794324
## la1511_S_noacc_9-la1511_C_noacc_9 1.0000000
## m058_C_1acc_9-la1511_C_noacc_9    0.9944085
## m058_C_5acc_9-la1511_C_noacc_9    0.9999679
## m058_C_noacc_9-la1511_C_noacc_9   1.0000000
## m058_S_1acc_9-la1511_C_noacc_9    0.9999890
## m058_S_5acc_9-la1511_C_noacc_9    1.0000000
## m058_S_noacc_9-la1511_C_noacc_9   0.7261485
## m248_C_1acc_9-la1511_C_noacc_9    0.9998565
## m248_C_5acc_9-la1511_C_noacc_9    0.4795681
## m248_C_noacc_9-la1511_C_noacc_9   0.6982588
## m248_S_1acc_9-la1511_C_noacc_9    0.9832135
## m248_S_5acc_9-la1511_C_noacc_9    0.8688005
## m248_S_noacc_9-la1511_C_noacc_9   0.2909910
## la1511_S_5acc_9-la1511_S_1acc_9   0.9999986
## la1511_S_noacc_9-la1511_S_1acc_9  0.9937333
## m058_C_1acc_9-la1511_S_1acc_9     1.0000000
## m058_C_5acc_9-la1511_S_1acc_9     1.0000000
## m058_C_noacc_9-la1511_S_1acc_9    0.9977366
## m058_S_1acc_9-la1511_S_1acc_9     1.0000000
## m058_S_5acc_9-la1511_S_1acc_9     0.9999974
## m058_S_noacc_9-la1511_S_1acc_9    0.9999904
## m248_C_1acc_9-la1511_S_1acc_9     1.0000000
## m248_C_5acc_9-la1511_S_1acc_9     0.9992773
## m248_C_noacc_9-la1511_S_1acc_9    0.9999819
## m248_S_1acc_9-la1511_S_1acc_9     1.0000000
## m248_S_5acc_9-la1511_S_1acc_9     0.9999999
## m248_S_noacc_9-la1511_S_1acc_9    0.9920340
## la1511_S_noacc_9-la1511_S_5acc_9  0.7378010
## m058_C_1acc_9-la1511_S_5acc_9     0.9999993
## m058_C_5acc_9-la1511_S_5acc_9     0.9990210
## m058_C_noacc_9-la1511_S_5acc_9    0.7767253
## m058_S_1acc_9-la1511_S_5acc_9     0.9981532
## m058_S_5acc_9-la1511_S_5acc_9     0.9731329
## m058_S_noacc_9-la1511_S_5acc_9    1.0000000
## m248_C_1acc_9-la1511_S_5acc_9     0.9996827
## m248_C_5acc_9-la1511_S_5acc_9     1.0000000
## m248_C_noacc_9-la1511_S_5acc_9    1.0000000
## m248_S_1acc_9-la1511_S_5acc_9     1.0000000
## m248_S_5acc_9-la1511_S_5acc_9     1.0000000
## m248_S_noacc_9-la1511_S_5acc_9    1.0000000
## m058_C_1acc_9-la1511_S_noacc_9    0.9652438
## m058_C_5acc_9-la1511_S_noacc_9    0.9989330
## m058_C_noacc_9-la1511_S_noacc_9   1.0000000
## m058_S_1acc_9-la1511_S_noacc_9    0.9994802
## m058_S_5acc_9-la1511_S_noacc_9    0.9999979
## m058_S_noacc_9-la1511_S_noacc_9   0.5193611
## m248_C_1acc_9-la1511_S_noacc_9    0.9970624
## m248_C_5acc_9-la1511_S_noacc_9    0.2900794
## m248_C_noacc_9-la1511_S_noacc_9   0.4893893
## m248_S_1acc_9-la1511_S_noacc_9    0.9259963
## m248_S_5acc_9-la1511_S_noacc_9    0.6997962
## m248_S_noacc_9-la1511_S_noacc_9   0.1545264
## m058_C_5acc_9-m058_C_1acc_9       1.0000000
## m058_C_noacc_9-m058_C_1acc_9      0.9802048
## m058_S_1acc_9-m058_C_1acc_9       1.0000000
## m058_S_5acc_9-m058_C_1acc_9       0.9999080
## m058_S_noacc_9-m058_C_1acc_9      0.9999930
## m248_C_1acc_9-m058_C_1acc_9       1.0000000
## m248_C_5acc_9-m058_C_1acc_9       0.9990964
## m248_C_noacc_9-m058_C_1acc_9      0.9999855
## m248_S_1acc_9-m058_C_1acc_9       1.0000000
## m248_S_5acc_9-m058_C_1acc_9       1.0000000
## m248_S_noacc_9-m058_C_1acc_9      0.9882238
## m058_C_noacc_9-m058_C_5acc_9      0.9997820
## m058_S_1acc_9-m058_C_5acc_9       1.0000000
## m058_S_5acc_9-m058_C_5acc_9       1.0000000
## m058_S_noacc_9-m058_C_5acc_9      0.9938808
## m248_C_1acc_9-m058_C_5acc_9       1.0000000
## m248_C_5acc_9-m058_C_5acc_9       0.9405656
## m248_C_noacc_9-m058_C_5acc_9      0.9914363
## m248_S_1acc_9-m058_C_5acc_9       0.9999995
## m248_S_5acc_9-m058_C_5acc_9       0.9995114
## m248_S_noacc_9-m058_C_5acc_9      0.8063533
## m058_S_1acc_9-m058_C_noacc_9      0.9999173
## m058_S_5acc_9-m058_C_noacc_9      1.0000000
## m058_S_noacc_9-m058_C_noacc_9     0.5275992
## m248_C_1acc_9-m058_C_noacc_9      0.9991645
## m248_C_5acc_9-m058_C_noacc_9      0.2766542
## m248_C_noacc_9-m058_C_noacc_9     0.4944991
## m248_S_1acc_9-m058_C_noacc_9      0.9494715
## m248_S_5acc_9-m058_C_noacc_9      0.7246557
## m248_S_noacc_9-m058_C_noacc_9     0.1357666
## m058_S_5acc_9-m058_S_1acc_9       1.0000000
## m058_S_noacc_9-m058_S_1acc_9      0.9893546
## m248_C_1acc_9-m058_S_1acc_9       1.0000000
## m248_C_5acc_9-m058_S_1acc_9       0.9169623
## m248_C_noacc_9-m058_S_1acc_9      0.9855703
## m248_S_1acc_9-m058_S_1acc_9       0.9999979
## m248_S_5acc_9-m058_S_1acc_9       0.9989182
## m248_S_noacc_9-m058_S_1acc_9      0.7604141
## m058_S_noacc_9-m058_S_5acc_9      0.9004767
## m248_C_1acc_9-m058_S_5acc_9       1.0000000
## m248_C_5acc_9-m058_S_5acc_9       0.6892322
## m248_C_noacc_9-m058_S_5acc_9      0.8818263
## m248_S_1acc_9-m058_S_5acc_9       0.9992988
## m248_S_5acc_9-m058_S_5acc_9       0.9730278
## m248_S_noacc_9-m058_S_5acc_9      0.4601392
## m248_C_1acc_9-m058_S_noacc_9      0.9977453
## m248_C_5acc_9-m058_S_noacc_9      1.0000000
## m248_C_noacc_9-m058_S_noacc_9     1.0000000
## m248_S_1acc_9-m058_S_noacc_9      0.9999998
## m248_S_5acc_9-m058_S_noacc_9      1.0000000
## m248_S_noacc_9-m058_S_noacc_9     0.9999997
## m248_C_5acc_9-m248_C_1acc_9       0.9675780
## m248_C_noacc_9-m248_C_1acc_9      0.9966576
## m248_S_1acc_9-m248_C_1acc_9       1.0000000
## m248_S_5acc_9-m248_C_1acc_9       0.9998841
## m248_S_noacc_9-m248_C_1acc_9      0.8688979
## m248_C_noacc_9-m248_C_5acc_9      1.0000000
## m248_S_1acc_9-m248_C_5acc_9       0.9998733
## m248_S_5acc_9-m248_C_5acc_9       0.9999999
## m248_S_noacc_9-m248_C_5acc_9      1.0000000
## m248_S_1acc_9-m248_C_noacc_9      0.9999994
## m248_S_5acc_9-m248_C_noacc_9      1.0000000
## m248_S_noacc_9-m248_C_noacc_9     0.9999999
## m248_S_5acc_9-m248_S_1acc_9       1.0000000
## m248_S_noacc_9-m248_S_1acc_9      0.9968157
## m248_S_noacc_9-m248_S_5acc_9      0.9999616
P5 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P5)
stat.test
## $Letters
##  la1511_C_5acc_9 la1511_C_noacc_9  la1511_S_1acc_9  la1511_S_5acc_9 
##              "a"              "a"              "a"              "a" 
## la1511_S_noacc_9    m058_C_1acc_9    m058_C_5acc_9   m058_C_noacc_9 
##              "a"              "a"              "a"              "a" 
##    m058_S_1acc_9    m058_S_5acc_9   m058_S_noacc_9    m248_C_1acc_9 
##              "a"              "a"              "a"              "a" 
##    m248_C_5acc_9   m248_C_noacc_9    m248_S_1acc_9    m248_S_5acc_9 
##              "a"              "a"              "a"              "a" 
##   m248_S_noacc_9  la1511_C_1acc_9 
##              "a"              "a" 
## 
## $LetterMatrix
##                     a
## la1511_C_5acc_9  TRUE
## la1511_C_noacc_9 TRUE
## la1511_S_1acc_9  TRUE
## la1511_S_5acc_9  TRUE
## la1511_S_noacc_9 TRUE
## m058_C_1acc_9    TRUE
## m058_C_5acc_9    TRUE
## m058_C_noacc_9   TRUE
## m058_S_1acc_9    TRUE
## m058_S_5acc_9    TRUE
## m058_S_noacc_9   TRUE
## m248_C_1acc_9    TRUE
## m248_C_5acc_9    TRUE
## m248_C_noacc_9   TRUE
## m248_S_1acc_9    TRUE
## m248_S_5acc_9    TRUE
## m248_S_noacc_9   TRUE
## la1511_C_1acc_9  TRUE
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ACC_pareto_location3 <- subset(ACC_pareto_location2, ACC_pareto_location2$pareto.front.scaling.distanc < 2)

ACC_pareto_distance_graph <- ggplot(data = ACC_pareto_location3, mapping = aes(x = All.ID, y = pareto.front.scaling.distance
, colour = Condition.all)) 
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + ylab("Pareto front scaling distance") + xlab("") #+ ggtitle("")
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 2.5)
ACC_pareto_distance_graph

ACC_pareto_distance_graph <- ggplot(data=ACC_pareto_location3, aes(x= Condition.all, y=pareto.front.scaling.distance, color = Condition.all)) 
ACC_pareto_distance_graph <- ACC_pareto_distance_graph +  geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
ACC_pareto_distance_graph <- ACC_pareto_distance_graph + facet_grid(~ Accessions )

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