20230508_cyto_pareto-front_components
This is a pareto-front components calculation for 3 tomatoes experienced cytokinin and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20221118_RSA_M248M058LA1511_cyto_100mM_Salt_2days. The root tracing was done by Trent Donaldson in March 2023.
getwd()## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20230508_cyto_pareto-front_components"list.files(pattern = ".csv")## [1] "Pareto-Cyto-both-scaling-nonscaling-analyzed.csv"cyto_pareto_location <-read.csv("Pareto-Cyto-both-scaling-nonscaling-analyzed.csv")
cyto_pareto_locationcyto_pareto_location$Condition.all <- paste(cyto_pareto_location$Condition, cyto_pareto_location$Condition2, sep="_")
cyto_pareto_locationlibrary(ggplot2)
library(ggpubr)
library(multcompView)cyto_pareto_location$All.ID <- paste(cyto_pareto_location$Accessions, cyto_pareto_location$Condition.all, cyto_pareto_location$Day, sep="_")
cyto_pareto_locationcyto_pareto_location2 <- subset(cyto_pareto_location, cyto_pareto_location$Day > 5)
cyto_pareto_location2aov(pareto.front.scaling.location ~ All.ID, data = cyto_pareto_location2)## Call:
## aov(formula = pareto.front.scaling.location ~ All.ID, data = cyto_pareto_location2)
##
## Terms:
## All.ID Residuals
## Sum of Squares 6.284438 7.527507
## Deg. of Freedom 17 142
##
## Residual standard error: 0.2302403
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(pareto.front.scaling.location ~ All.ID, data = cyto_pareto_location2))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = pareto.front.scaling.location ~ All.ID, data = cyto_pareto_location2)
##
## $All.ID
## diff lwr upr
## LA1511_C_locyto_9-LA1511_C_hicyto_9 -0.043000000 -0.408962514 0.322962514
## LA1511_C_nocyto_9-LA1511_C_hicyto_9 -0.288000000 -0.710577112 0.134577112
## LA1511_S_hicyto_9-LA1511_C_hicyto_9 0.003666667 -0.372324074 0.379657407
## LA1511_S_locyto_9-LA1511_C_hicyto_9 0.069222222 -0.306768519 0.445212963
## LA1511_S_nocyto_9-LA1511_C_hicyto_9 -0.325222222 -0.701212963 0.050768519
## M058_C_hicyto_9-LA1511_C_hicyto_9 0.168250000 -0.219911863 0.556411863
## M058_C_locyto_9-LA1511_C_hicyto_9 0.185000000 -0.180962514 0.550962514
## M058_C_nocyto_9-LA1511_C_hicyto_9 -0.063000000 -0.428962514 0.302962514
## M058_S_hicyto_9-LA1511_C_hicyto_9 0.112000000 -0.276161863 0.500161863
## M058_S_locyto_9-LA1511_C_hicyto_9 0.178000000 -0.187962514 0.543962514
## M058_S_nocyto_9-LA1511_C_hicyto_9 -0.470500000 -0.954622900 0.013622900
## M248_C_hicyto_9-LA1511_C_hicyto_9 0.126000000 -0.239962514 0.491962514
## M248_C_locyto_9-LA1511_C_hicyto_9 0.128000000 -0.237962514 0.493962514
## M248_C_nocyto_9-LA1511_C_hicyto_9 -0.161000000 -0.526962514 0.204962514
## M248_S_hicyto_9-LA1511_C_hicyto_9 0.175750000 -0.212411863 0.563911863
## M248_S_locyto_9-LA1511_C_hicyto_9 0.079222222 -0.296768519 0.455212963
## M248_S_nocyto_9-LA1511_C_hicyto_9 -0.449000000 -0.814962514 -0.083037486
## LA1511_C_nocyto_9-LA1511_C_locyto_9 -0.245000000 -0.667577112 0.177577112
## LA1511_S_hicyto_9-LA1511_C_locyto_9 0.046666667 -0.329324074 0.422657407
## LA1511_S_locyto_9-LA1511_C_locyto_9 0.112222222 -0.263768519 0.488212963
## LA1511_S_nocyto_9-LA1511_C_locyto_9 -0.282222222 -0.658212963 0.093768519
## M058_C_hicyto_9-LA1511_C_locyto_9 0.211250000 -0.176911863 0.599411863
## M058_C_locyto_9-LA1511_C_locyto_9 0.228000000 -0.137962514 0.593962514
## M058_C_nocyto_9-LA1511_C_locyto_9 -0.020000000 -0.385962514 0.345962514
## M058_S_hicyto_9-LA1511_C_locyto_9 0.155000000 -0.233161863 0.543161863
## M058_S_locyto_9-LA1511_C_locyto_9 0.221000000 -0.144962514 0.586962514
## M058_S_nocyto_9-LA1511_C_locyto_9 -0.427500000 -0.911622900 0.056622900
## M248_C_hicyto_9-LA1511_C_locyto_9 0.169000000 -0.196962514 0.534962514
## M248_C_locyto_9-LA1511_C_locyto_9 0.171000000 -0.194962514 0.536962514
## M248_C_nocyto_9-LA1511_C_locyto_9 -0.118000000 -0.483962514 0.247962514
## M248_S_hicyto_9-LA1511_C_locyto_9 0.218750000 -0.169411863 0.606911863
## M248_S_locyto_9-LA1511_C_locyto_9 0.122222222 -0.253768519 0.498212963
## M248_S_nocyto_9-LA1511_C_locyto_9 -0.406000000 -0.771962514 -0.040037486
## LA1511_S_hicyto_9-LA1511_C_nocyto_9 0.291666667 -0.139624292 0.722957625
## LA1511_S_locyto_9-LA1511_C_nocyto_9 0.357222222 -0.074068736 0.788513181
## LA1511_S_nocyto_9-LA1511_C_nocyto_9 -0.037222222 -0.468513181 0.394068736
## M058_C_hicyto_9-LA1511_C_nocyto_9 0.456250000 0.014308278 0.898191722
## M058_C_locyto_9-LA1511_C_nocyto_9 0.473000000 0.050422888 0.895577112
## M058_C_nocyto_9-LA1511_C_nocyto_9 0.225000000 -0.197577112 0.647577112
## M058_S_hicyto_9-LA1511_C_nocyto_9 0.400000000 -0.041941722 0.841941722
## M058_S_locyto_9-LA1511_C_nocyto_9 0.466000000 0.043422888 0.888577112
## M058_S_nocyto_9-LA1511_C_nocyto_9 -0.182500000 -0.710721390 0.345721390
## M248_C_hicyto_9-LA1511_C_nocyto_9 0.414000000 -0.008577112 0.836577112
## M248_C_locyto_9-LA1511_C_nocyto_9 0.416000000 -0.006577112 0.838577112
## M248_C_nocyto_9-LA1511_C_nocyto_9 0.127000000 -0.295577112 0.549577112
## M248_S_hicyto_9-LA1511_C_nocyto_9 0.463750000 0.021808278 0.905691722
## M248_S_locyto_9-LA1511_C_nocyto_9 0.367222222 -0.064068736 0.798513181
## M248_S_nocyto_9-LA1511_C_nocyto_9 -0.161000000 -0.583577112 0.261577112
## LA1511_S_locyto_9-LA1511_S_hicyto_9 0.065555556 -0.320202805 0.451313916
## LA1511_S_nocyto_9-LA1511_S_hicyto_9 -0.328888889 -0.714647249 0.056869472
## M058_C_hicyto_9-LA1511_S_hicyto_9 0.164583333 -0.233047283 0.562213950
## M058_C_locyto_9-LA1511_S_hicyto_9 0.181333333 -0.194657407 0.557324074
## M058_C_nocyto_9-LA1511_S_hicyto_9 -0.066666667 -0.442657407 0.309324074
## M058_S_hicyto_9-LA1511_S_hicyto_9 0.108333333 -0.289297283 0.505963950
## M058_S_locyto_9-LA1511_S_hicyto_9 0.174333333 -0.201657407 0.550324074
## M058_S_nocyto_9-LA1511_S_hicyto_9 -0.474166667 -0.965914019 0.017580685
## M248_C_hicyto_9-LA1511_S_hicyto_9 0.122333333 -0.253657407 0.498324074
## M248_C_locyto_9-LA1511_S_hicyto_9 0.124333333 -0.251657407 0.500324074
## M248_C_nocyto_9-LA1511_S_hicyto_9 -0.164666667 -0.540657407 0.211324074
## M248_S_hicyto_9-LA1511_S_hicyto_9 0.172083333 -0.225547283 0.569713950
## M248_S_locyto_9-LA1511_S_hicyto_9 0.075555556 -0.310202805 0.461313916
## M248_S_nocyto_9-LA1511_S_hicyto_9 -0.452666667 -0.828657407 -0.076675926
## LA1511_S_nocyto_9-LA1511_S_locyto_9 -0.394444444 -0.780202805 -0.008686084
## M058_C_hicyto_9-LA1511_S_locyto_9 0.099027778 -0.298602839 0.496658394
## M058_C_locyto_9-LA1511_S_locyto_9 0.115777778 -0.260212963 0.491768519
## M058_C_nocyto_9-LA1511_S_locyto_9 -0.132222222 -0.508212963 0.243768519
## M058_S_hicyto_9-LA1511_S_locyto_9 0.042777778 -0.354852839 0.440408394
## M058_S_locyto_9-LA1511_S_locyto_9 0.108777778 -0.267212963 0.484768519
## M058_S_nocyto_9-LA1511_S_locyto_9 -0.539722222 -1.031469574 -0.047974870
## M248_C_hicyto_9-LA1511_S_locyto_9 0.056777778 -0.319212963 0.432768519
## M248_C_locyto_9-LA1511_S_locyto_9 0.058777778 -0.317212963 0.434768519
## M248_C_nocyto_9-LA1511_S_locyto_9 -0.230222222 -0.606212963 0.145768519
## M248_S_hicyto_9-LA1511_S_locyto_9 0.106527778 -0.291102839 0.504158394
## M248_S_locyto_9-LA1511_S_locyto_9 0.010000000 -0.375758361 0.395758361
## M248_S_nocyto_9-LA1511_S_locyto_9 -0.518222222 -0.894212963 -0.142231481
## M058_C_hicyto_9-LA1511_S_nocyto_9 0.493472222 0.095841606 0.891102839
## M058_C_locyto_9-LA1511_S_nocyto_9 0.510222222 0.134231481 0.886212963
## M058_C_nocyto_9-LA1511_S_nocyto_9 0.262222222 -0.113768519 0.638212963
## M058_S_hicyto_9-LA1511_S_nocyto_9 0.437222222 0.039591606 0.834852839
## M058_S_locyto_9-LA1511_S_nocyto_9 0.503222222 0.127231481 0.879212963
## M058_S_nocyto_9-LA1511_S_nocyto_9 -0.145277778 -0.637025130 0.346469574
## M248_C_hicyto_9-LA1511_S_nocyto_9 0.451222222 0.075231481 0.827212963
## M248_C_locyto_9-LA1511_S_nocyto_9 0.453222222 0.077231481 0.829212963
## M248_C_nocyto_9-LA1511_S_nocyto_9 0.164222222 -0.211768519 0.540212963
## M248_S_hicyto_9-LA1511_S_nocyto_9 0.500972222 0.103341606 0.898602839
## M248_S_locyto_9-LA1511_S_nocyto_9 0.404444444 0.018686084 0.790202805
## M248_S_nocyto_9-LA1511_S_nocyto_9 -0.123777778 -0.499768519 0.252212963
## M058_C_locyto_9-M058_C_hicyto_9 0.016750000 -0.371411863 0.404911863
## M058_C_nocyto_9-M058_C_hicyto_9 -0.231250000 -0.619411863 0.156911863
## M058_S_hicyto_9-M058_C_hicyto_9 -0.056250000 -0.465408529 0.352908529
## M058_S_locyto_9-M058_C_hicyto_9 0.009750000 -0.378411863 0.397911863
## M058_S_nocyto_9-M058_C_hicyto_9 -0.638750000 -1.139864810 -0.137635190
## M248_C_hicyto_9-M058_C_hicyto_9 -0.042250000 -0.430411863 0.345911863
## M248_C_locyto_9-M058_C_hicyto_9 -0.040250000 -0.428411863 0.347911863
## M248_C_nocyto_9-M058_C_hicyto_9 -0.329250000 -0.717411863 0.058911863
## M248_S_hicyto_9-M058_C_hicyto_9 0.007500000 -0.401658529 0.416658529
## M248_S_locyto_9-M058_C_hicyto_9 -0.089027778 -0.486658394 0.308602839
## M248_S_nocyto_9-M058_C_hicyto_9 -0.617250000 -1.005411863 -0.229088137
## M058_C_nocyto_9-M058_C_locyto_9 -0.248000000 -0.613962514 0.117962514
## M058_S_hicyto_9-M058_C_locyto_9 -0.073000000 -0.461161863 0.315161863
## M058_S_locyto_9-M058_C_locyto_9 -0.007000000 -0.372962514 0.358962514
## M058_S_nocyto_9-M058_C_locyto_9 -0.655500000 -1.139622900 -0.171377100
## M248_C_hicyto_9-M058_C_locyto_9 -0.059000000 -0.424962514 0.306962514
## M248_C_locyto_9-M058_C_locyto_9 -0.057000000 -0.422962514 0.308962514
## M248_C_nocyto_9-M058_C_locyto_9 -0.346000000 -0.711962514 0.019962514
## M248_S_hicyto_9-M058_C_locyto_9 -0.009250000 -0.397411863 0.378911863
## M248_S_locyto_9-M058_C_locyto_9 -0.105777778 -0.481768519 0.270212963
## M248_S_nocyto_9-M058_C_locyto_9 -0.634000000 -0.999962514 -0.268037486
## M058_S_hicyto_9-M058_C_nocyto_9 0.175000000 -0.213161863 0.563161863
## M058_S_locyto_9-M058_C_nocyto_9 0.241000000 -0.124962514 0.606962514
## M058_S_nocyto_9-M058_C_nocyto_9 -0.407500000 -0.891622900 0.076622900
## M248_C_hicyto_9-M058_C_nocyto_9 0.189000000 -0.176962514 0.554962514
## M248_C_locyto_9-M058_C_nocyto_9 0.191000000 -0.174962514 0.556962514
## M248_C_nocyto_9-M058_C_nocyto_9 -0.098000000 -0.463962514 0.267962514
## M248_S_hicyto_9-M058_C_nocyto_9 0.238750000 -0.149411863 0.626911863
## M248_S_locyto_9-M058_C_nocyto_9 0.142222222 -0.233768519 0.518212963
## M248_S_nocyto_9-M058_C_nocyto_9 -0.386000000 -0.751962514 -0.020037486
## M058_S_locyto_9-M058_S_hicyto_9 0.066000000 -0.322161863 0.454161863
## M058_S_nocyto_9-M058_S_hicyto_9 -0.582500000 -1.083614810 -0.081385190
## M248_C_hicyto_9-M058_S_hicyto_9 0.014000000 -0.374161863 0.402161863
## M248_C_locyto_9-M058_S_hicyto_9 0.016000000 -0.372161863 0.404161863
## M248_C_nocyto_9-M058_S_hicyto_9 -0.273000000 -0.661161863 0.115161863
## M248_S_hicyto_9-M058_S_hicyto_9 0.063750000 -0.345408529 0.472908529
## M248_S_locyto_9-M058_S_hicyto_9 -0.032777778 -0.430408394 0.364852839
## M248_S_nocyto_9-M058_S_hicyto_9 -0.561000000 -0.949161863 -0.172838137
## M058_S_nocyto_9-M058_S_locyto_9 -0.648500000 -1.132622900 -0.164377100
## M248_C_hicyto_9-M058_S_locyto_9 -0.052000000 -0.417962514 0.313962514
## M248_C_locyto_9-M058_S_locyto_9 -0.050000000 -0.415962514 0.315962514
## M248_C_nocyto_9-M058_S_locyto_9 -0.339000000 -0.704962514 0.026962514
## M248_S_hicyto_9-M058_S_locyto_9 -0.002250000 -0.390411863 0.385911863
## M248_S_locyto_9-M058_S_locyto_9 -0.098777778 -0.474768519 0.277212963
## M248_S_nocyto_9-M058_S_locyto_9 -0.627000000 -0.992962514 -0.261037486
## M248_C_hicyto_9-M058_S_nocyto_9 0.596500000 0.112377100 1.080622900
## M248_C_locyto_9-M058_S_nocyto_9 0.598500000 0.114377100 1.082622900
## M248_C_nocyto_9-M058_S_nocyto_9 0.309500000 -0.174622900 0.793622900
## M248_S_hicyto_9-M058_S_nocyto_9 0.646250000 0.145135190 1.147364810
## M248_S_locyto_9-M058_S_nocyto_9 0.549722222 0.057974870 1.041469574
## M248_S_nocyto_9-M058_S_nocyto_9 0.021500000 -0.462622900 0.505622900
## M248_C_locyto_9-M248_C_hicyto_9 0.002000000 -0.363962514 0.367962514
## M248_C_nocyto_9-M248_C_hicyto_9 -0.287000000 -0.652962514 0.078962514
## M248_S_hicyto_9-M248_C_hicyto_9 0.049750000 -0.338411863 0.437911863
## M248_S_locyto_9-M248_C_hicyto_9 -0.046777778 -0.422768519 0.329212963
## M248_S_nocyto_9-M248_C_hicyto_9 -0.575000000 -0.940962514 -0.209037486
## M248_C_nocyto_9-M248_C_locyto_9 -0.289000000 -0.654962514 0.076962514
## M248_S_hicyto_9-M248_C_locyto_9 0.047750000 -0.340411863 0.435911863
## M248_S_locyto_9-M248_C_locyto_9 -0.048777778 -0.424768519 0.327212963
## M248_S_nocyto_9-M248_C_locyto_9 -0.577000000 -0.942962514 -0.211037486
## M248_S_hicyto_9-M248_C_nocyto_9 0.336750000 -0.051411863 0.724911863
## M248_S_locyto_9-M248_C_nocyto_9 0.240222222 -0.135768519 0.616212963
## M248_S_nocyto_9-M248_C_nocyto_9 -0.288000000 -0.653962514 0.077962514
## M248_S_locyto_9-M248_S_hicyto_9 -0.096527778 -0.494158394 0.301102839
## M248_S_nocyto_9-M248_S_hicyto_9 -0.624750000 -1.012911863 -0.236588137
## M248_S_nocyto_9-M248_S_locyto_9 -0.528222222 -0.904212963 -0.152231481
## p adj
## LA1511_C_locyto_9-LA1511_C_hicyto_9 1.0000000
## LA1511_C_nocyto_9-LA1511_C_hicyto_9 0.5924427
## LA1511_S_hicyto_9-LA1511_C_hicyto_9 1.0000000
## LA1511_S_locyto_9-LA1511_C_hicyto_9 0.9999999
## LA1511_S_nocyto_9-LA1511_C_hicyto_9 0.1810901
## M058_C_hicyto_9-LA1511_C_hicyto_9 0.9859808
## M058_C_locyto_9-LA1511_C_hicyto_9 0.9408612
## M058_C_nocyto_9-LA1511_C_hicyto_9 1.0000000
## M058_S_hicyto_9-LA1511_C_hicyto_9 0.9998979
## M058_S_locyto_9-LA1511_C_hicyto_9 0.9576843
## M058_S_nocyto_9-LA1511_C_hicyto_9 0.0670416
## M248_C_hicyto_9-LA1511_C_hicyto_9 0.9989773
## M248_C_locyto_9-LA1511_C_hicyto_9 0.9987581
## M248_C_nocyto_9-LA1511_C_hicyto_9 0.9836999
## M248_S_hicyto_9-LA1511_C_hicyto_9 0.9783202
## M248_S_locyto_9-LA1511_C_hicyto_9 0.9999989
## M248_S_nocyto_9-LA1511_C_hicyto_9 0.0031488
## LA1511_C_nocyto_9-LA1511_C_locyto_9 0.8334749
## LA1511_S_hicyto_9-LA1511_C_locyto_9 1.0000000
## LA1511_S_locyto_9-LA1511_C_locyto_9 0.9998386
## LA1511_S_nocyto_9-LA1511_C_locyto_9 0.4125281
## M058_C_hicyto_9-LA1511_C_locyto_9 0.8935229
## M058_C_locyto_9-LA1511_C_locyto_9 0.7407904
## M058_C_nocyto_9-LA1511_C_locyto_9 1.0000000
## M058_S_hicyto_9-LA1511_C_locyto_9 0.9941543
## M058_S_locyto_9-LA1511_C_locyto_9 0.7841650
## M058_S_nocyto_9-LA1511_C_locyto_9 0.1552868
## M248_C_hicyto_9-LA1511_C_locyto_9 0.9737784
## M248_C_locyto_9-LA1511_C_locyto_9 0.9706914
## M248_C_nocyto_9-LA1511_C_locyto_9 0.9995539
## M248_S_hicyto_9-LA1511_C_locyto_9 0.8628368
## M248_S_locyto_9-LA1511_C_locyto_9 0.9995048
## M248_S_nocyto_9-LA1511_C_locyto_9 0.0143181
## LA1511_S_hicyto_9-LA1511_C_nocyto_9 0.6063679
## LA1511_S_locyto_9-LA1511_C_nocyto_9 0.2427854
## LA1511_S_nocyto_9-LA1511_C_nocyto_9 1.0000000
## M058_C_hicyto_9-LA1511_C_nocyto_9 0.0351506
## M058_C_locyto_9-LA1511_C_nocyto_9 0.0126813
## M058_C_nocyto_9-LA1511_C_nocyto_9 0.9099092
## M058_S_hicyto_9-LA1511_C_nocyto_9 0.1276736
## M058_S_locyto_9-LA1511_C_nocyto_9 0.0155205
## M058_S_nocyto_9-LA1511_C_nocyto_9 0.9989322
## M248_C_hicyto_9-LA1511_C_nocyto_9 0.0618569
## M248_C_locyto_9-LA1511_C_nocyto_9 0.0588962
## M248_C_nocyto_9-LA1511_C_nocyto_9 0.9998230
## M248_S_hicyto_9-LA1511_C_nocyto_9 0.0290440
## M248_S_locyto_9-LA1511_C_nocyto_9 0.2023597
## M248_S_nocyto_9-LA1511_C_nocyto_9 0.9965625
## LA1511_S_locyto_9-LA1511_S_hicyto_9 1.0000000
## LA1511_S_nocyto_9-LA1511_S_hicyto_9 0.2005201
## M058_C_hicyto_9-LA1511_S_hicyto_9 0.9913554
## M058_C_locyto_9-LA1511_S_hicyto_9 0.9607823
## M058_C_nocyto_9-LA1511_S_hicyto_9 0.9999999
## M058_S_hicyto_9-LA1511_S_hicyto_9 0.9999538
## M058_S_locyto_9-LA1511_S_hicyto_9 0.9727527
## M058_S_nocyto_9-LA1511_S_hicyto_9 0.0724215
## M248_C_hicyto_9-LA1511_S_hicyto_9 0.9994990
## M248_C_locyto_9-LA1511_S_hicyto_9 0.9993837
## M248_C_nocyto_9-LA1511_S_hicyto_9 0.9844263
## M248_S_hicyto_9-LA1511_S_hicyto_9 0.9862049
## M248_S_locyto_9-LA1511_S_hicyto_9 0.9999996
## M248_S_nocyto_9-LA1511_S_hicyto_9 0.0042876
## LA1511_S_nocyto_9-LA1511_S_locyto_9 0.0391968
## M058_C_hicyto_9-LA1511_S_locyto_9 0.9999871
## M058_C_locyto_9-LA1511_S_locyto_9 0.9997555
## M058_C_nocyto_9-LA1511_S_locyto_9 0.9986729
## M058_S_hicyto_9-LA1511_S_locyto_9 1.0000000
## M058_S_locyto_9-LA1511_S_locyto_9 0.9998941
## M058_S_nocyto_9-LA1511_S_locyto_9 0.0165241
## M248_C_hicyto_9-LA1511_S_locyto_9 1.0000000
## M248_C_locyto_9-LA1511_S_locyto_9 1.0000000
## M248_C_nocyto_9-LA1511_S_locyto_9 0.7654914
## M248_S_hicyto_9-LA1511_S_locyto_9 0.9999635
## M248_S_locyto_9-LA1511_S_locyto_9 1.0000000
## M248_S_nocyto_9-LA1511_S_locyto_9 0.0003597
## M058_C_hicyto_9-LA1511_S_nocyto_9 0.0025968
## M058_C_locyto_9-LA1511_S_nocyto_9 0.0004944
## M058_C_nocyto_9-LA1511_S_nocyto_9 0.5502867
## M058_S_hicyto_9-LA1511_S_nocyto_9 0.0161294
## M058_S_locyto_9-LA1511_S_nocyto_9 0.0006510
## M058_S_nocyto_9-LA1511_S_nocyto_9 0.9998594
## M248_C_hicyto_9-LA1511_S_nocyto_9 0.0045121
## M248_C_locyto_9-LA1511_S_nocyto_9 0.0042040
## M248_C_nocyto_9-LA1511_S_nocyto_9 0.9848473
## M248_S_hicyto_9-LA1511_S_nocyto_9 0.0020011
## M248_S_locyto_9-LA1511_S_nocyto_9 0.0293446
## M248_S_nocyto_9-LA1511_S_nocyto_9 0.9994179
## M058_C_locyto_9-M058_C_hicyto_9 1.0000000
## M058_C_nocyto_9-M058_C_hicyto_9 0.8015081
## M058_S_hicyto_9-M058_C_hicyto_9 1.0000000
## M058_S_locyto_9-M058_C_hicyto_9 1.0000000
## M058_S_nocyto_9-M058_C_hicyto_9 0.0016277
## M248_C_hicyto_9-M058_C_hicyto_9 1.0000000
## M248_C_locyto_9-M058_C_hicyto_9 1.0000000
## M248_C_nocyto_9-M058_C_hicyto_9 0.2076742
## M248_S_hicyto_9-M058_C_hicyto_9 1.0000000
## M248_S_locyto_9-M058_C_hicyto_9 0.9999973
## M248_S_nocyto_9-M058_C_hicyto_9 0.0000123
## M058_C_nocyto_9-M058_C_locyto_9 0.6026702
## M058_S_hicyto_9-M058_C_locyto_9 0.9999998
## M058_S_locyto_9-M058_C_locyto_9 1.0000000
## M058_S_nocyto_9-M058_C_locyto_9 0.0005171
## M248_C_hicyto_9-M058_C_locyto_9 1.0000000
## M248_C_locyto_9-M058_C_locyto_9 1.0000000
## M248_C_nocyto_9-M058_C_locyto_9 0.0872752
## M248_S_hicyto_9-M058_C_locyto_9 1.0000000
## M248_S_locyto_9-M058_C_locyto_9 0.9999278
## M248_S_nocyto_9-M058_C_locyto_9 0.0000011
## M058_S_hicyto_9-M058_C_nocyto_9 0.9792080
## M058_S_locyto_9-M058_C_nocyto_9 0.6526929
## M058_S_nocyto_9-M058_C_nocyto_9 0.2186965
## M248_C_hicyto_9-M058_C_nocyto_9 0.9293648
## M248_C_locyto_9-M058_C_nocyto_9 0.9230764
## M248_C_nocyto_9-M058_C_nocyto_9 0.9999637
## M248_S_hicyto_9-M058_C_nocyto_9 0.7591994
## M248_S_locyto_9-M058_C_nocyto_9 0.9968372
## M248_S_nocyto_9-M058_C_nocyto_9 0.0273074
## M058_S_locyto_9-M058_S_hicyto_9 1.0000000
## M058_S_nocyto_9-M058_S_hicyto_9 0.0073784
## M248_C_hicyto_9-M058_S_hicyto_9 1.0000000
## M248_C_locyto_9-M058_S_hicyto_9 1.0000000
## M248_C_nocyto_9-M058_S_hicyto_9 0.5346390
## M248_S_hicyto_9-M058_S_hicyto_9 1.0000000
## M248_S_locyto_9-M058_S_hicyto_9 1.0000000
## M248_S_nocyto_9-M058_S_hicyto_9 0.0001287
## M058_S_nocyto_9-M058_S_locyto_9 0.0006401
## M248_C_hicyto_9-M058_S_locyto_9 1.0000000
## M248_C_locyto_9-M058_S_locyto_9 1.0000000
## M248_C_nocyto_9-M058_S_locyto_9 0.1048853
## M248_S_hicyto_9-M058_S_locyto_9 1.0000000
## M248_S_locyto_9-M058_S_locyto_9 0.9999723
## M248_S_nocyto_9-M058_S_locyto_9 0.0000015
## M248_C_hicyto_9-M058_S_nocyto_9 0.0029330
## M248_C_locyto_9-M058_S_nocyto_9 0.0027723
## M248_C_nocyto_9-M058_S_nocyto_9 0.7014160
## M248_S_hicyto_9-M058_S_nocyto_9 0.0013172
## M248_S_locyto_9-M058_S_nocyto_9 0.0129057
## M248_S_nocyto_9-M058_S_nocyto_9 1.0000000
## M248_C_locyto_9-M248_C_hicyto_9 1.0000000
## M248_C_nocyto_9-M248_C_hicyto_9 0.3330447
## M248_S_hicyto_9-M248_C_hicyto_9 1.0000000
## M248_S_locyto_9-M248_C_hicyto_9 1.0000000
## M248_S_nocyto_9-M248_C_hicyto_9 0.0000169
## M248_C_nocyto_9-M248_C_locyto_9 0.3209284
## M248_S_hicyto_9-M248_C_locyto_9 1.0000000
## M248_S_locyto_9-M248_C_locyto_9 1.0000000
## M248_S_nocyto_9-M248_C_locyto_9 0.0000155
## M248_S_hicyto_9-M248_C_nocyto_9 0.1772296
## M248_S_locyto_9-M248_C_nocyto_9 0.7023959
## M248_S_nocyto_9-M248_C_nocyto_9 0.3269560
## M248_S_locyto_9-M248_S_hicyto_9 0.9999911
## M248_S_nocyto_9-M248_S_hicyto_9 0.0000089
## M248_S_nocyto_9-M248_S_locyto_9 0.0002403P6 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P6)
stat.test## LA1511_C_locyto_9 LA1511_C_nocyto_9 LA1511_S_hicyto_9 LA1511_S_locyto_9
## "abc" "abd" "abc" "ac"
## LA1511_S_nocyto_9 M058_C_hicyto_9 M058_C_locyto_9 M058_C_nocyto_9
## "bd" "c" "c" "abc"
## M058_S_hicyto_9 M058_S_locyto_9 M058_S_nocyto_9 M248_C_hicyto_9
## "ac" "c" "bd" "ac"
## M248_C_locyto_9 M248_C_nocyto_9 M248_S_hicyto_9 M248_S_locyto_9
## "ac" "abcd" "c" "ac"
## M248_S_nocyto_9 LA1511_C_hicyto_9
## "d" "abc"test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testcyto_pareto_location2$Condition.all <- factor(cyto_pareto_location2$Condition.all, levels = c("C_nocyto", "C_locyto","C_hicyto", "S_nocyto","S_locyto","S_hicyto"))
cyto_pareto_location_graph <- ggplot(data = cyto_pareto_location2, mapping = aes(x = All.ID, y = pareto.front.scaling.location
, colour = Condition.all))
cyto_pareto_location_graph <- cyto_pareto_location_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
cyto_pareto_location_graph <- cyto_pareto_location_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
cyto_pareto_location_graph <- cyto_pareto_location_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
cyto_pareto_location_graph <- cyto_pareto_location_graph + ylab("Pareto front location") + xlab("") #+ ggtitle("")
cyto_pareto_location_graph <- cyto_pareto_location_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
cyto_pareto_location_graph <- cyto_pareto_location_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 1.5)
cyto_pareto_location_graph
cyto_pareto_location_graph <- ggplot(data=cyto_pareto_location2, aes(x= Condition.all, y=pareto.front.scaling.location, color = Condition.all))
cyto_pareto_location_graph <- cyto_pareto_location_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
cyto_pareto_location_graph <- cyto_pareto_location_graph + facet_grid(~ Accessions )
cyto_pareto_location_graph <- cyto_pareto_location_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
cyto_pareto_location_graph <- cyto_pareto_location_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
cyto_pareto_location_graph <- cyto_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))
cyto_pareto_location_graph
aov(pareto.front.scaling.distance ~ All.ID, data = cyto_pareto_location2)## Call:
## aov(formula = pareto.front.scaling.distance ~ All.ID, data = cyto_pareto_location2)
##
## Terms:
## All.ID Residuals
## Sum of Squares 0.737033 3.816516
## Deg. of Freedom 17 142
##
## Residual standard error: 0.1639417
## Estimated effects may be unbalancedOutput <- TukeyHSD(aov(pareto.front.scaling.distance ~ All.ID, data = cyto_pareto_location2))
Output## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = pareto.front.scaling.distance ~ All.ID, data = cyto_pareto_location2)
##
## $All.ID
## diff lwr upr
## LA1511_C_locyto_9-LA1511_C_hicyto_9 -0.096661800 -0.35724391 0.16392031
## LA1511_C_nocyto_9-LA1511_C_hicyto_9 -0.133102000 -0.43399630 0.16779230
## LA1511_S_hicyto_9-LA1511_C_hicyto_9 0.016501889 -0.25122077 0.28422455
## LA1511_S_locyto_9-LA1511_C_hicyto_9 0.065164000 -0.20255866 0.33288666
## LA1511_S_nocyto_9-LA1511_C_hicyto_9 -0.134543000 -0.40226566 0.13317966
## M058_C_hicyto_9-LA1511_C_hicyto_9 0.073319125 -0.20306994 0.34970819
## M058_C_locyto_9-LA1511_C_hicyto_9 -0.125954900 -0.38653701 0.13462721
## M058_C_nocyto_9-LA1511_C_hicyto_9 -0.140510600 -0.40109271 0.12007151
## M058_S_hicyto_9-LA1511_C_hicyto_9 -0.068793375 -0.34518244 0.20759569
## M058_S_locyto_9-LA1511_C_hicyto_9 -0.045137400 -0.30571951 0.21544471
## M058_S_nocyto_9-LA1511_C_hicyto_9 -0.076764750 -0.42148247 0.26795297
## M248_C_hicyto_9-LA1511_C_hicyto_9 -0.100999600 -0.36158171 0.15958251
## M248_C_locyto_9-LA1511_C_hicyto_9 -0.127463000 -0.38804511 0.13311911
## M248_C_nocyto_9-LA1511_C_hicyto_9 -0.116048400 -0.37663051 0.14453371
## M248_S_hicyto_9-LA1511_C_hicyto_9 0.028887750 -0.24750131 0.30527681
## M248_S_locyto_9-LA1511_C_hicyto_9 -0.069859556 -0.33758222 0.19786311
## M248_S_nocyto_9-LA1511_C_hicyto_9 -0.073697700 -0.33427981 0.18688441
## LA1511_C_nocyto_9-LA1511_C_locyto_9 -0.036440200 -0.33733450 0.26445410
## LA1511_S_hicyto_9-LA1511_C_locyto_9 0.113163689 -0.15455897 0.38088635
## LA1511_S_locyto_9-LA1511_C_locyto_9 0.161825800 -0.10589686 0.42954846
## LA1511_S_nocyto_9-LA1511_C_locyto_9 -0.037881200 -0.30560386 0.22984146
## M058_C_hicyto_9-LA1511_C_locyto_9 0.169980925 -0.10640814 0.44636999
## M058_C_locyto_9-LA1511_C_locyto_9 -0.029293100 -0.28987521 0.23128901
## M058_C_nocyto_9-LA1511_C_locyto_9 -0.043848800 -0.30443091 0.21673331
## M058_S_hicyto_9-LA1511_C_locyto_9 0.027868425 -0.24852064 0.30425749
## M058_S_locyto_9-LA1511_C_locyto_9 0.051524400 -0.20905771 0.31210651
## M058_S_nocyto_9-LA1511_C_locyto_9 0.019897050 -0.32482067 0.36461477
## M248_C_hicyto_9-LA1511_C_locyto_9 -0.004337800 -0.26491991 0.25624431
## M248_C_locyto_9-LA1511_C_locyto_9 -0.030801200 -0.29138331 0.22978091
## M248_C_nocyto_9-LA1511_C_locyto_9 -0.019386600 -0.27996871 0.24119551
## M248_S_hicyto_9-LA1511_C_locyto_9 0.125549550 -0.15083951 0.40193861
## M248_S_locyto_9-LA1511_C_locyto_9 0.026802244 -0.24092042 0.29452491
## M248_S_nocyto_9-LA1511_C_locyto_9 0.022964100 -0.23761801 0.28354621
## LA1511_S_hicyto_9-LA1511_C_nocyto_9 0.149603889 -0.15749507 0.45670285
## LA1511_S_locyto_9-LA1511_C_nocyto_9 0.198266000 -0.10883296 0.50536496
## LA1511_S_nocyto_9-LA1511_C_nocyto_9 -0.001441000 -0.30853996 0.30565796
## M058_C_hicyto_9-LA1511_C_nocyto_9 0.206421125 -0.10826166 0.52110391
## M058_C_locyto_9-LA1511_C_nocyto_9 0.007147100 -0.29374720 0.30804140
## M058_C_nocyto_9-LA1511_C_nocyto_9 -0.007408600 -0.30830290 0.29348570
## M058_S_hicyto_9-LA1511_C_nocyto_9 0.064308625 -0.25037416 0.37899141
## M058_S_locyto_9-LA1511_C_nocyto_9 0.087964600 -0.21292970 0.38885890
## M058_S_nocyto_9-LA1511_C_nocyto_9 0.056337250 -0.31978062 0.43245512
## M248_C_hicyto_9-LA1511_C_nocyto_9 0.032102400 -0.26879190 0.33299670
## M248_C_locyto_9-LA1511_C_nocyto_9 0.005639000 -0.29525530 0.30653330
## M248_C_nocyto_9-LA1511_C_nocyto_9 0.017053600 -0.28384070 0.31794790
## M248_S_hicyto_9-LA1511_C_nocyto_9 0.161989750 -0.15269304 0.47667254
## M248_S_locyto_9-LA1511_C_nocyto_9 0.063242444 -0.24385651 0.37034140
## M248_S_nocyto_9-LA1511_C_nocyto_9 0.059404300 -0.24149000 0.36029860
## LA1511_S_locyto_9-LA1511_S_hicyto_9 0.048662111 -0.22601555 0.32333977
## LA1511_S_nocyto_9-LA1511_S_hicyto_9 -0.151044889 -0.42572255 0.12363277
## M058_C_hicyto_9-LA1511_S_hicyto_9 0.056817236 -0.22631401 0.33994848
## M058_C_locyto_9-LA1511_S_hicyto_9 -0.142456789 -0.41017945 0.12526587
## M058_C_nocyto_9-LA1511_S_hicyto_9 -0.157012489 -0.42473515 0.11071017
## M058_S_hicyto_9-LA1511_S_hicyto_9 -0.085295264 -0.36842651 0.19783598
## M058_S_locyto_9-LA1511_S_hicyto_9 -0.061639289 -0.32936195 0.20608337
## M058_S_nocyto_9-LA1511_S_hicyto_9 -0.093266639 -0.44341332 0.25688004
## M248_C_hicyto_9-LA1511_S_hicyto_9 -0.117501489 -0.38522415 0.15022117
## M248_C_locyto_9-LA1511_S_hicyto_9 -0.143964889 -0.41168755 0.12375777
## M248_C_nocyto_9-LA1511_S_hicyto_9 -0.132550289 -0.40027295 0.13517237
## M248_S_hicyto_9-LA1511_S_hicyto_9 0.012385861 -0.27074539 0.29551711
## M248_S_locyto_9-LA1511_S_hicyto_9 -0.086361444 -0.36103910 0.18831621
## M248_S_nocyto_9-LA1511_S_hicyto_9 -0.090199589 -0.35792225 0.17752307
## LA1511_S_nocyto_9-LA1511_S_locyto_9 -0.199707000 -0.47438466 0.07497066
## M058_C_hicyto_9-LA1511_S_locyto_9 0.008155125 -0.27497612 0.29128637
## M058_C_locyto_9-LA1511_S_locyto_9 -0.191118900 -0.45884156 0.07660376
## M058_C_nocyto_9-LA1511_S_locyto_9 -0.205674600 -0.47339726 0.06204806
## M058_S_hicyto_9-LA1511_S_locyto_9 -0.133957375 -0.41708862 0.14917387
## M058_S_locyto_9-LA1511_S_locyto_9 -0.110301400 -0.37802406 0.15742126
## M058_S_nocyto_9-LA1511_S_locyto_9 -0.141928750 -0.49207543 0.20821793
## M248_C_hicyto_9-LA1511_S_locyto_9 -0.166163600 -0.43388626 0.10155906
## M248_C_locyto_9-LA1511_S_locyto_9 -0.192627000 -0.46034966 0.07509566
## M248_C_nocyto_9-LA1511_S_locyto_9 -0.181212400 -0.44893506 0.08651026
## M248_S_hicyto_9-LA1511_S_locyto_9 -0.036276250 -0.31940750 0.24685500
## M248_S_locyto_9-LA1511_S_locyto_9 -0.135023556 -0.40970121 0.13965410
## M248_S_nocyto_9-LA1511_S_locyto_9 -0.138861700 -0.40658436 0.12886096
## M058_C_hicyto_9-LA1511_S_nocyto_9 0.207862125 -0.07526912 0.49099337
## M058_C_locyto_9-LA1511_S_nocyto_9 0.008588100 -0.25913456 0.27631076
## M058_C_nocyto_9-LA1511_S_nocyto_9 -0.005967600 -0.27369026 0.26175506
## M058_S_hicyto_9-LA1511_S_nocyto_9 0.065749625 -0.21738162 0.34888087
## M058_S_locyto_9-LA1511_S_nocyto_9 0.089405600 -0.17831706 0.35712826
## M058_S_nocyto_9-LA1511_S_nocyto_9 0.057778250 -0.29236843 0.40792493
## M248_C_hicyto_9-LA1511_S_nocyto_9 0.033543400 -0.23417926 0.30126606
## M248_C_locyto_9-LA1511_S_nocyto_9 0.007080000 -0.26064266 0.27480266
## M248_C_nocyto_9-LA1511_S_nocyto_9 0.018494600 -0.24922806 0.28621726
## M248_S_hicyto_9-LA1511_S_nocyto_9 0.163430750 -0.11970050 0.44656200
## M248_S_locyto_9-LA1511_S_nocyto_9 0.064683444 -0.20999421 0.33936110
## M248_S_nocyto_9-LA1511_S_nocyto_9 0.060845300 -0.20687736 0.32856796
## M058_C_locyto_9-M058_C_hicyto_9 -0.199274025 -0.47566309 0.07711504
## M058_C_nocyto_9-M058_C_hicyto_9 -0.213829725 -0.49021879 0.06255934
## M058_S_hicyto_9-M058_C_hicyto_9 -0.142112500 -0.43345215 0.14922715
## M058_S_locyto_9-M058_C_hicyto_9 -0.118456525 -0.39484559 0.15793254
## M058_S_nocyto_9-M058_C_hicyto_9 -0.150083875 -0.50690062 0.20673287
## M248_C_hicyto_9-M058_C_hicyto_9 -0.174318725 -0.45070779 0.10207034
## M248_C_locyto_9-M058_C_hicyto_9 -0.200782125 -0.47717119 0.07560694
## M248_C_nocyto_9-M058_C_hicyto_9 -0.189367525 -0.46575659 0.08702154
## M248_S_hicyto_9-M058_C_hicyto_9 -0.044431375 -0.33577103 0.24690828
## M248_S_locyto_9-M058_C_hicyto_9 -0.143178681 -0.42630993 0.13995257
## M248_S_nocyto_9-M058_C_hicyto_9 -0.147016825 -0.42340589 0.12937224
## M058_C_nocyto_9-M058_C_locyto_9 -0.014555700 -0.27513781 0.24602641
## M058_S_hicyto_9-M058_C_locyto_9 0.057161525 -0.21922754 0.33355059
## M058_S_locyto_9-M058_C_locyto_9 0.080817500 -0.17976461 0.34139961
## M058_S_nocyto_9-M058_C_locyto_9 0.049190150 -0.29552757 0.39390787
## M248_C_hicyto_9-M058_C_locyto_9 0.024955300 -0.23562681 0.28553741
## M248_C_locyto_9-M058_C_locyto_9 -0.001508100 -0.26209021 0.25907401
## M248_C_nocyto_9-M058_C_locyto_9 0.009906500 -0.25067561 0.27048861
## M248_S_hicyto_9-M058_C_locyto_9 0.154842650 -0.12154641 0.43123171
## M248_S_locyto_9-M058_C_locyto_9 0.056095344 -0.21162732 0.32381801
## M248_S_nocyto_9-M058_C_locyto_9 0.052257200 -0.20832491 0.31283931
## M058_S_hicyto_9-M058_C_nocyto_9 0.071717225 -0.20467184 0.34810629
## M058_S_locyto_9-M058_C_nocyto_9 0.095373200 -0.16520891 0.35595531
## M058_S_nocyto_9-M058_C_nocyto_9 0.063745850 -0.28097187 0.40846357
## M248_C_hicyto_9-M058_C_nocyto_9 0.039511000 -0.22107111 0.30009311
## M248_C_locyto_9-M058_C_nocyto_9 0.013047600 -0.24753451 0.27362971
## M248_C_nocyto_9-M058_C_nocyto_9 0.024462200 -0.23611991 0.28504431
## M248_S_hicyto_9-M058_C_nocyto_9 0.169398350 -0.10699071 0.44578741
## M248_S_locyto_9-M058_C_nocyto_9 0.070651044 -0.19707162 0.33837371
## M248_S_nocyto_9-M058_C_nocyto_9 0.066812900 -0.19376921 0.32739501
## M058_S_locyto_9-M058_S_hicyto_9 0.023655975 -0.25273309 0.30004504
## M058_S_nocyto_9-M058_S_hicyto_9 -0.007971375 -0.36478812 0.34884537
## M248_C_hicyto_9-M058_S_hicyto_9 -0.032206225 -0.30859529 0.24418284
## M248_C_locyto_9-M058_S_hicyto_9 -0.058669625 -0.33505869 0.21771944
## M248_C_nocyto_9-M058_S_hicyto_9 -0.047255025 -0.32364409 0.22913404
## M248_S_hicyto_9-M058_S_hicyto_9 0.097681125 -0.19365853 0.38902078
## M248_S_locyto_9-M058_S_hicyto_9 -0.001066181 -0.28419743 0.28206507
## M248_S_nocyto_9-M058_S_hicyto_9 -0.004904325 -0.28129339 0.27148474
## M058_S_nocyto_9-M058_S_locyto_9 -0.031627350 -0.37634507 0.31309037
## M248_C_hicyto_9-M058_S_locyto_9 -0.055862200 -0.31644431 0.20471991
## M248_C_locyto_9-M058_S_locyto_9 -0.082325600 -0.34290771 0.17825651
## M248_C_nocyto_9-M058_S_locyto_9 -0.070911000 -0.33149311 0.18967111
## M248_S_hicyto_9-M058_S_locyto_9 0.074025150 -0.20236391 0.35041421
## M248_S_locyto_9-M058_S_locyto_9 -0.024722156 -0.29244482 0.24300051
## M248_S_nocyto_9-M058_S_locyto_9 -0.028560300 -0.28914241 0.23202181
## M248_C_hicyto_9-M058_S_nocyto_9 -0.024234850 -0.36895257 0.32048287
## M248_C_locyto_9-M058_S_nocyto_9 -0.050698250 -0.39541597 0.29401947
## M248_C_nocyto_9-M058_S_nocyto_9 -0.039283650 -0.38400137 0.30543407
## M248_S_hicyto_9-M058_S_nocyto_9 0.105652500 -0.25116424 0.46246924
## M248_S_locyto_9-M058_S_nocyto_9 0.006905194 -0.34324149 0.35705188
## M248_S_nocyto_9-M058_S_nocyto_9 0.003067050 -0.34165067 0.34778477
## M248_C_locyto_9-M248_C_hicyto_9 -0.026463400 -0.28704551 0.23411871
## M248_C_nocyto_9-M248_C_hicyto_9 -0.015048800 -0.27563091 0.24553331
## M248_S_hicyto_9-M248_C_hicyto_9 0.129887350 -0.14650171 0.40627641
## M248_S_locyto_9-M248_C_hicyto_9 0.031140044 -0.23658262 0.29886271
## M248_S_nocyto_9-M248_C_hicyto_9 0.027301900 -0.23328021 0.28788401
## M248_C_nocyto_9-M248_C_locyto_9 0.011414600 -0.24916751 0.27199671
## M248_S_hicyto_9-M248_C_locyto_9 0.156350750 -0.12003831 0.43273981
## M248_S_locyto_9-M248_C_locyto_9 0.057603444 -0.21011922 0.32532611
## M248_S_nocyto_9-M248_C_locyto_9 0.053765300 -0.20681681 0.31434741
## M248_S_hicyto_9-M248_C_nocyto_9 0.144936150 -0.13145291 0.42132521
## M248_S_locyto_9-M248_C_nocyto_9 0.046188844 -0.22153382 0.31391151
## M248_S_nocyto_9-M248_C_nocyto_9 0.042350700 -0.21823141 0.30293281
## M248_S_locyto_9-M248_S_hicyto_9 -0.098747306 -0.38187855 0.18438394
## M248_S_nocyto_9-M248_S_hicyto_9 -0.102585450 -0.37897451 0.17380361
## M248_S_nocyto_9-M248_S_locyto_9 -0.003838144 -0.27156081 0.26388452
## p adj
## LA1511_C_locyto_9-LA1511_C_hicyto_9 0.9974821
## LA1511_C_nocyto_9-LA1511_C_hicyto_9 0.9827770
## LA1511_S_hicyto_9-LA1511_C_hicyto_9 1.0000000
## LA1511_S_locyto_9-LA1511_C_hicyto_9 0.9999907
## LA1511_S_nocyto_9-LA1511_C_hicyto_9 0.9437424
## M058_C_hicyto_9-LA1511_C_hicyto_9 0.9999682
## M058_C_locyto_9-LA1511_C_hicyto_9 0.9599857
## M058_C_nocyto_9-LA1511_C_hicyto_9 0.9007098
## M058_S_hicyto_9-LA1511_C_hicyto_9 0.9999872
## M058_S_locyto_9-LA1511_C_hicyto_9 0.9999999
## M058_S_nocyto_9-LA1511_C_hicyto_9 0.9999975
## M248_C_hicyto_9-LA1511_C_hicyto_9 0.9958162
## M248_C_locyto_9-LA1511_C_hicyto_9 0.9555049
## M248_C_nocyto_9-LA1511_C_hicyto_9 0.9815804
## M248_S_hicyto_9-LA1511_C_hicyto_9 1.0000000
## M248_S_locyto_9-LA1511_C_hicyto_9 0.9999748
## M248_S_nocyto_9-LA1511_C_hicyto_9 0.9999224
## LA1511_C_nocyto_9-LA1511_C_locyto_9 1.0000000
## LA1511_S_hicyto_9-LA1511_C_locyto_9 0.9891985
## LA1511_S_locyto_9-LA1511_C_locyto_9 0.7829318
## LA1511_S_nocyto_9-LA1511_C_locyto_9 1.0000000
## M058_C_hicyto_9-LA1511_C_locyto_9 0.7593649
## M058_C_locyto_9-LA1511_C_locyto_9 1.0000000
## M058_C_nocyto_9-LA1511_C_locyto_9 1.0000000
## M058_S_hicyto_9-LA1511_C_locyto_9 1.0000000
## M058_S_locyto_9-LA1511_C_locyto_9 0.9999996
## M058_S_nocyto_9-LA1511_C_locyto_9 1.0000000
## M248_C_hicyto_9-LA1511_C_locyto_9 1.0000000
## M248_C_locyto_9-LA1511_C_locyto_9 1.0000000
## M248_C_nocyto_9-LA1511_C_locyto_9 1.0000000
## M248_S_hicyto_9-LA1511_C_locyto_9 0.9776231
## M248_S_locyto_9-LA1511_C_locyto_9 1.0000000
## M248_S_nocyto_9-LA1511_C_locyto_9 1.0000000
## LA1511_S_hicyto_9-LA1511_C_nocyto_9 0.9570892
## LA1511_S_locyto_9-LA1511_C_nocyto_9 0.6856650
## LA1511_S_nocyto_9-LA1511_C_nocyto_9 1.0000000
## M058_C_hicyto_9-LA1511_C_nocyto_9 0.6593175
## M058_C_locyto_9-LA1511_C_nocyto_9 1.0000000
## M058_C_nocyto_9-LA1511_C_nocyto_9 1.0000000
## M058_S_hicyto_9-LA1511_C_nocyto_9 0.9999993
## M058_S_locyto_9-LA1511_C_nocyto_9 0.9998780
## M058_S_nocyto_9-LA1511_C_nocyto_9 1.0000000
## M248_C_hicyto_9-LA1511_C_nocyto_9 1.0000000
## M248_C_locyto_9-LA1511_C_nocyto_9 1.0000000
## M248_C_nocyto_9-LA1511_C_nocyto_9 1.0000000
## M248_S_hicyto_9-LA1511_C_nocyto_9 0.9312190
## M248_S_locyto_9-LA1511_C_nocyto_9 0.9999992
## M248_S_nocyto_9-LA1511_C_nocyto_9 0.9999996
## LA1511_S_locyto_9-LA1511_S_hicyto_9 0.9999999
## LA1511_S_nocyto_9-LA1511_S_hicyto_9 0.8850139
## M058_C_hicyto_9-LA1511_S_hicyto_9 0.9999995
## M058_C_locyto_9-LA1511_S_hicyto_9 0.9103576
## M058_C_nocyto_9-LA1511_S_hicyto_9 0.8204303
## M058_S_hicyto_9-LA1511_S_hicyto_9 0.9998172
## M058_S_locyto_9-LA1511_S_hicyto_9 0.9999959
## M058_S_nocyto_9-LA1511_S_hicyto_9 0.9999663
## M248_C_hicyto_9-LA1511_S_hicyto_9 0.9840856
## M248_C_locyto_9-LA1511_S_hicyto_9 0.9027693
## M248_C_nocyto_9-LA1511_S_hicyto_9 0.9505216
## M248_S_hicyto_9-LA1511_S_hicyto_9 1.0000000
## M248_S_locyto_9-LA1511_S_hicyto_9 0.9996785
## M248_S_nocyto_9-LA1511_S_hicyto_9 0.9992197
## LA1511_S_nocyto_9-LA1511_S_locyto_9 0.4722941
## M058_C_hicyto_9-LA1511_S_locyto_9 1.0000000
## M058_C_locyto_9-LA1511_S_locyto_9 0.5067566
## M058_C_nocyto_9-LA1511_S_locyto_9 0.3698571
## M058_S_hicyto_9-LA1511_S_locyto_9 0.9670774
## M058_S_locyto_9-LA1511_S_locyto_9 0.9917747
## M058_S_nocyto_9-LA1511_S_locyto_9 0.9931074
## M248_C_hicyto_9-LA1511_S_locyto_9 0.7463198
## M248_C_locyto_9-LA1511_S_locyto_9 0.4919745
## M248_C_nocyto_9-LA1511_S_locyto_9 0.6047796
## M248_S_hicyto_9-LA1511_S_locyto_9 1.0000000
## M248_S_locyto_9-LA1511_S_locyto_9 0.9535233
## M248_S_nocyto_9-LA1511_S_locyto_9 0.9268418
## M058_C_hicyto_9-LA1511_S_nocyto_9 0.4540119
## M058_C_locyto_9-LA1511_S_nocyto_9 1.0000000
## M058_C_nocyto_9-LA1511_S_nocyto_9 1.0000000
## M058_S_hicyto_9-LA1511_S_nocyto_9 0.9999953
## M058_S_locyto_9-LA1511_S_nocyto_9 0.9993020
## M058_S_nocyto_9-LA1511_S_nocyto_9 1.0000000
## M248_C_hicyto_9-LA1511_S_nocyto_9 1.0000000
## M248_C_locyto_9-LA1511_S_nocyto_9 1.0000000
## M248_C_nocyto_9-LA1511_S_nocyto_9 1.0000000
## M248_S_hicyto_9-LA1511_S_nocyto_9 0.8383013
## M248_S_locyto_9-LA1511_S_nocyto_9 0.9999943
## M248_S_nocyto_9-LA1511_S_nocyto_9 0.9999966
## M058_C_locyto_9-M058_C_hicyto_9 0.4880822
## M058_C_nocyto_9-M058_C_hicyto_9 0.3571729
## M058_S_hicyto_9-M058_C_hicyto_9 0.9565874
## M058_S_locyto_9-M058_C_hicyto_9 0.9875196
## M058_S_nocyto_9-M058_C_hicyto_9 0.9897429
## M248_C_hicyto_9-M058_C_hicyto_9 0.7224574
## M248_C_locyto_9-M058_C_hicyto_9 0.4738806
## M248_C_nocyto_9-M058_C_hicyto_9 0.5828603
## M248_S_hicyto_9-M058_C_hicyto_9 1.0000000
## M248_S_locyto_9-M058_C_hicyto_9 0.9406824
## M248_S_nocyto_9-M058_C_hicyto_9 0.9106013
## M058_C_nocyto_9-M058_C_locyto_9 1.0000000
## M058_S_hicyto_9-M058_C_locyto_9 0.9999992
## M058_S_locyto_9-M058_C_locyto_9 0.9997313
## M058_S_nocyto_9-M058_C_locyto_9 1.0000000
## M248_C_hicyto_9-M058_C_locyto_9 1.0000000
## M248_C_locyto_9-M058_C_locyto_9 1.0000000
## M248_C_nocyto_9-M058_C_locyto_9 1.0000000
## M248_S_hicyto_9-M058_C_locyto_9 0.8684440
## M248_S_locyto_9-M058_C_locyto_9 0.9999990
## M248_S_nocyto_9-M058_C_locyto_9 0.9999995
## M058_S_hicyto_9-M058_C_nocyto_9 0.9999768
## M058_S_locyto_9-M058_C_nocyto_9 0.9978516
## M058_S_nocyto_9-M058_C_nocyto_9 0.9999999
## M248_C_hicyto_9-M058_C_nocyto_9 1.0000000
## M248_C_locyto_9-M058_C_nocyto_9 1.0000000
## M248_C_nocyto_9-M058_C_nocyto_9 1.0000000
## M248_S_hicyto_9-M058_C_nocyto_9 0.7641575
## M248_S_locyto_9-M058_C_nocyto_9 0.9999705
## M248_S_nocyto_9-M058_C_nocyto_9 0.9999804
## M058_S_locyto_9-M058_S_hicyto_9 1.0000000
## M058_S_nocyto_9-M058_S_hicyto_9 1.0000000
## M248_C_hicyto_9-M058_S_hicyto_9 1.0000000
## M248_C_locyto_9-M058_S_hicyto_9 0.9999988
## M248_C_nocyto_9-M058_S_hicyto_9 1.0000000
## M248_S_hicyto_9-M058_S_hicyto_9 0.9992660
## M248_S_locyto_9-M058_S_hicyto_9 1.0000000
## M248_S_nocyto_9-M058_S_hicyto_9 1.0000000
## M058_S_nocyto_9-M058_S_locyto_9 1.0000000
## M248_C_hicyto_9-M058_S_locyto_9 0.9999986
## M248_C_locyto_9-M058_S_locyto_9 0.9996576
## M248_C_nocyto_9-M058_S_locyto_9 0.9999545
## M248_S_hicyto_9-M058_S_locyto_9 0.9999636
## M248_S_locyto_9-M058_S_locyto_9 1.0000000
## M248_S_nocyto_9-M058_S_locyto_9 1.0000000
## M248_C_hicyto_9-M058_S_nocyto_9 1.0000000
## M248_C_locyto_9-M058_S_nocyto_9 1.0000000
## M248_C_nocyto_9-M058_S_nocyto_9 1.0000000
## M248_S_hicyto_9-M058_S_nocyto_9 0.9998551
## M248_S_locyto_9-M058_S_nocyto_9 1.0000000
## M248_S_nocyto_9-M058_S_nocyto_9 1.0000000
## M248_C_locyto_9-M248_C_hicyto_9 1.0000000
## M248_C_nocyto_9-M248_C_hicyto_9 1.0000000
## M248_S_hicyto_9-M248_C_hicyto_9 0.9690783
## M248_S_locyto_9-M248_C_hicyto_9 1.0000000
## M248_S_nocyto_9-M248_C_hicyto_9 1.0000000
## M248_C_nocyto_9-M248_C_locyto_9 1.0000000
## M248_S_hicyto_9-M248_C_locyto_9 0.8591533
## M248_S_locyto_9-M248_C_locyto_9 0.9999985
## M248_S_nocyto_9-M248_C_locyto_9 0.9999992
## M248_S_hicyto_9-M248_C_nocyto_9 0.9201011
## M248_S_locyto_9-M248_C_nocyto_9 1.0000000
## M248_S_nocyto_9-M248_C_nocyto_9 1.0000000
## M248_S_locyto_9-M248_S_hicyto_9 0.9988008
## M248_S_nocyto_9-M248_S_hicyto_9 0.9974647
## M248_S_nocyto_9-M248_S_locyto_9 1.0000000P5 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P5)
stat.test## $Letters
## LA1511_C_locyto_9 LA1511_C_nocyto_9 LA1511_S_hicyto_9 LA1511_S_locyto_9
## "a" "a" "a" "a"
## LA1511_S_nocyto_9 M058_C_hicyto_9 M058_C_locyto_9 M058_C_nocyto_9
## "a" "a" "a" "a"
## M058_S_hicyto_9 M058_S_locyto_9 M058_S_nocyto_9 M248_C_hicyto_9
## "a" "a" "a" "a"
## M248_C_locyto_9 M248_C_nocyto_9 M248_S_hicyto_9 M248_S_locyto_9
## "a" "a" "a" "a"
## M248_S_nocyto_9 LA1511_C_hicyto_9
## "a" "a"
##
## $LetterMatrix
## a
## LA1511_C_locyto_9 TRUE
## LA1511_C_nocyto_9 TRUE
## LA1511_S_hicyto_9 TRUE
## LA1511_S_locyto_9 TRUE
## LA1511_S_nocyto_9 TRUE
## M058_C_hicyto_9 TRUE
## M058_C_locyto_9 TRUE
## M058_C_nocyto_9 TRUE
## M058_S_hicyto_9 TRUE
## M058_S_locyto_9 TRUE
## M058_S_nocyto_9 TRUE
## M248_C_hicyto_9 TRUE
## M248_C_locyto_9 TRUE
## M248_C_nocyto_9 TRUE
## M248_S_hicyto_9 TRUE
## M248_S_locyto_9 TRUE
## M248_S_nocyto_9 TRUE
## LA1511_C_hicyto_9 TRUEtest <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
testcyto_pareto_location3 <- subset(cyto_pareto_location2, cyto_pareto_location2$pareto.front.scaling.distanc < 2)
cyto_pareto_distance_graph <- ggplot(data = cyto_pareto_location3, mapping = aes(x = All.ID, y = pareto.front.scaling.distance
, colour = Condition.all))
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + ylab("Pareto front scaling distance") + xlab("") #+ ggtitle("")
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 2.5)
cyto_pareto_distance_graph
cyto_pareto_distance_graph <- ggplot(data=cyto_pareto_location3, aes(x= Condition.all, y=pareto.front.scaling.distance, color = Condition.all))
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + facet_grid(~ Accessions )
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
cyto_pareto_distance_graph <- cyto_pareto_distance_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
cyto_pareto_distance_graph <- cyto_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))
cyto_pareto_distance_graph