this experiment was performed on January 2022 in order to address whether there is a difference in tissue accumulation of the 3 tomato accessions, M248, M058, LA1511. These samples were grown similar to RSA set-up , 4 d on germination/control plates, d5 to +/- 100 mM salt, and then tissues including stem, leaves, and roots were harvested after 10 d on salt.

getwd()
## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20220617_ICP-MS_FW_DW_3tissues_M248M058LA1511_Plate_Grown"
setwd( "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20220617_ICP-MS_FW_DW_3tissues_M248M058LA1511_Plate_Grown/")
list.files(pattern = ".csv")
## [1] "20220124_root_leaf_stem_separated_ICP_LA1511_M058_M248_freshWeight v2.csv"          
## [2] "Eric04122022Rack 1 and 2 _3tomato_accessions_3tissue_types_plate_analyzed for R.csv"
ICP<- read.csv("Eric04122022Rack 1 and 2 _3tomato_accessions_3tissue_types_plate_analyzed for R.csv")
ICP
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 4.0.5
library(ggpubr)
## Warning: package 'ggpubr' was built under R version 4.0.5
library(multcompView)
## Warning: package 'multcompView' was built under R version 4.0.5
ICP$All.ID <- paste(ICP$Accession,ICP$Condition, ICP$Tissue,  sep="_")
ICP
aov(Na.con.mg.mg.dry.weight ~ All.ID, data = ICP)
## Call:
##    aov(formula = Na.con.mg.mg.dry.weight ~ All.ID, data = ICP)
## 
## Terms:
##                    All.ID Residuals
## Sum of Squares  280614.03  23341.32
## Deg. of Freedom        17       240
## 
## Residual standard error: 9.861821
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(Na.con.mg.mg.dry.weight ~ All.ID, data = ICP))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = Na.con.mg.mg.dry.weight ~ All.ID, data = ICP)
## 
## $All.ID
##                               diff          lwr        upr     p adj
## LA1511_C_R-LA1511_C_L  -0.28488585  -13.9292039  13.359432 1.0000000
## LA1511_C_S-LA1511_C_L   2.05162953  -11.5926885  15.695948 1.0000000
## LA1511_S_L-LA1511_C_L  28.63130032   14.9869823  42.275618 0.0000000
## LA1511_S_R-LA1511_C_L  29.84774507   16.2034270  43.492063 0.0000000
## LA1511_S_S-LA1511_C_L  75.40693021   61.7626122  89.051248 0.0000000
## M058_C_L-LA1511_C_L    -0.21686102  -13.3985246  12.964803 1.0000000
## M058_C_R-LA1511_C_L    -0.25547190  -13.4371354  12.926192 1.0000000
## M058_C_S-LA1511_C_L     2.27743473  -10.9042288  15.459098 1.0000000
## M058_S_L-LA1511_C_L    36.49229585   23.3106323  49.673959 0.0000000
## M058_S_R-LA1511_C_L    39.18417564   26.0025121  52.365839 0.0000000
## M058_S_S-LA1511_C_L    89.27833259   76.0966690 102.459996 0.0000000
## M248_C_L-LA1511_C_L     0.60734875  -12.5743148  13.789012 1.0000000
## M248_C_R-LA1511_C_L     0.46494316  -12.7167204  13.646607 1.0000000
## M248_C_S-LA1511_C_L     2.76074996  -10.4209136  15.942414 0.9999992
## M248_S_L-LA1511_C_L    54.09213468   40.9104711  67.273798 0.0000000
## M248_S_R-LA1511_C_L    41.23183183   28.0501683  54.413495 0.0000000
## M248_S_S-LA1511_C_L   102.77657585   89.5949123 115.958239 0.0000000
## LA1511_C_S-LA1511_C_R   2.33651538  -11.3078027  15.980833 1.0000000
## LA1511_S_L-LA1511_C_R  28.91618617   15.2718681  42.560504 0.0000000
## LA1511_S_R-LA1511_C_R  30.13263092   16.4883129  43.776949 0.0000000
## LA1511_S_S-LA1511_C_R  75.69181606   62.0474980  89.336134 0.0000000
## M058_C_L-LA1511_C_R     0.06802483  -13.1136387  13.249688 1.0000000
## M058_C_R-LA1511_C_R     0.02941395  -13.1522496  13.211078 1.0000000
## M058_C_S-LA1511_C_R     2.56232058  -10.6193430  15.743984 0.9999998
## M058_S_L-LA1511_C_R    36.77718170   23.5955182  49.958845 0.0000000
## M058_S_R-LA1511_C_R    39.46906149   26.2873979  52.650725 0.0000000
## M058_S_S-LA1511_C_R    89.56321844   76.3815549 102.744882 0.0000000
## M248_C_L-LA1511_C_R     0.89223460  -12.2894289  14.073898 1.0000000
## M248_C_R-LA1511_C_R     0.74982901  -12.4318345  13.931493 1.0000000
## M248_C_S-LA1511_C_R     3.04563581  -10.1360277  16.227299 0.9999966
## M248_S_L-LA1511_C_R    54.37702053   41.1953570  67.558684 0.0000000
## M248_S_R-LA1511_C_R    41.51671768   28.3350541  54.698381 0.0000000
## M248_S_S-LA1511_C_R   103.06146170   89.8797982 116.243125 0.0000000
## LA1511_S_L-LA1511_C_S  26.57967079   12.9353527  40.223989 0.0000000
## LA1511_S_R-LA1511_C_S  27.79611554   14.1517975  41.440434 0.0000000
## LA1511_S_S-LA1511_C_S  73.35530068   59.7109826  86.999619 0.0000000
## M058_C_L-LA1511_C_S    -2.26849055  -15.4501541  10.913173 1.0000000
## M058_C_R-LA1511_C_S    -2.30710143  -15.4887650  10.874562 1.0000000
## M058_C_S-LA1511_C_S     0.22580520  -12.9558583  13.407469 1.0000000
## M058_S_L-LA1511_C_S    34.44066632   21.2590028  47.622330 0.0000000
## M058_S_R-LA1511_C_S    37.13254611   23.9508826  50.314210 0.0000000
## M058_S_S-LA1511_C_S    87.22670306   74.0450395 100.408367 0.0000000
## M248_C_L-LA1511_C_S    -1.44428078  -14.6259443  11.737383 1.0000000
## M248_C_R-LA1511_C_S    -1.58668637  -14.7683499  11.594977 1.0000000
## M248_C_S-LA1511_C_S     0.70912043  -12.4725431  13.890784 1.0000000
## M248_S_L-LA1511_C_S    52.04050515   38.8588416  65.222169 0.0000000
## M248_S_R-LA1511_C_S    39.18020230   25.9985388  52.361866 0.0000000
## M248_S_S-LA1511_C_S   100.72494632   87.5432828 113.906610 0.0000000
## LA1511_S_R-LA1511_S_L   1.21644475  -12.4278733  14.860763 1.0000000
## LA1511_S_S-LA1511_S_L  46.77562990   33.1313119  60.419948 0.0000000
## M058_C_L-LA1511_S_L   -28.84816134  -42.0298249 -15.666498 0.0000000
## M058_C_R-LA1511_S_L   -28.88677221  -42.0684358 -15.705109 0.0000000
## M058_C_S-LA1511_S_L   -26.35386559  -39.5355291 -13.172202 0.0000000
## M058_S_L-LA1511_S_L     7.86099553   -5.3206680  21.042659 0.8115864
## M058_S_R-LA1511_S_L    10.55287532   -2.6287882  23.734539 0.3053025
## M058_S_S-LA1511_S_L    60.64703227   47.4653687  73.828696 0.0000000
## M248_C_L-LA1511_S_L   -28.02395157  -41.2056151 -14.842288 0.0000000
## M248_C_R-LA1511_S_L   -28.16635716  -41.3480207 -14.984694 0.0000000
## M248_C_S-LA1511_S_L   -25.87055036  -39.0522139 -12.688887 0.0000000
## M248_S_L-LA1511_S_L    25.46083436   12.2791708  38.642498 0.0000000
## M248_S_R-LA1511_S_L    12.60053151   -0.5811320  25.782195 0.0794857
## M248_S_S-LA1511_S_L    74.14527553   60.9636120  87.326939 0.0000000
## LA1511_S_S-LA1511_S_R  45.55918515   31.9148671  59.203503 0.0000000
## M058_C_L-LA1511_S_R   -30.06460609  -43.2462696 -16.882943 0.0000000
## M058_C_R-LA1511_S_R   -30.10321696  -43.2848805 -16.921553 0.0000000
## M058_C_S-LA1511_S_R   -27.57031034  -40.7519739 -14.388647 0.0000000
## M058_S_L-LA1511_S_R     6.64455078   -6.5371128  19.826214 0.9475774
## M058_S_R-LA1511_S_R     9.33643057   -3.8452330  22.518094 0.5339759
## M058_S_S-LA1511_S_R    59.43058752   46.2489240  72.612251 0.0000000
## M248_C_L-LA1511_S_R   -29.24039631  -42.4220599 -16.058733 0.0000000
## M248_C_R-LA1511_S_R   -29.38280191  -42.5644655 -16.201138 0.0000000
## M248_C_S-LA1511_S_R   -27.08699511  -40.2686587 -13.905332 0.0000000
## M248_S_L-LA1511_S_R    24.24438961   11.0627261  37.426053 0.0000001
## M248_S_R-LA1511_S_R    11.38408676   -1.7975768  24.565750 0.1872703
## M248_S_S-LA1511_S_R    72.92883078   59.7471672  86.110494 0.0000000
## M058_C_L-LA1511_S_S   -75.62379124  -88.8054548 -62.442128 0.0000000
## M058_C_R-LA1511_S_S   -75.66240211  -88.8440657 -62.480739 0.0000000
## M058_C_S-LA1511_S_S   -73.12949549  -86.3111590 -59.947832 0.0000000
## M058_S_L-LA1511_S_S   -38.91463437  -52.0962979 -25.732971 0.0000000
## M058_S_R-LA1511_S_S   -36.22275458  -49.4044181 -23.041091 0.0000000
## M058_S_S-LA1511_S_S    13.87140237    0.6897388  27.053066 0.0276694
## M248_C_L-LA1511_S_S   -74.79958146  -87.9812450 -61.617918 0.0000000
## M248_C_R-LA1511_S_S   -74.94198706  -88.1236506 -61.760324 0.0000000
## M248_C_S-LA1511_S_S   -72.64618025  -85.8278438 -59.464517 0.0000000
## M248_S_L-LA1511_S_S   -21.31479554  -34.4964591  -8.133132 0.0000051
## M248_S_R-LA1511_S_S   -34.17509839  -47.3567619 -20.993435 0.0000000
## M248_S_S-LA1511_S_S    27.36964563   14.1879821  40.551309 0.0000000
## M058_C_R-M058_C_L      -0.03861087  -12.7407797  12.663558 1.0000000
## M058_C_S-M058_C_L       2.49429575  -10.2078731  15.196465 0.9999997
## M058_S_L-M058_C_L      36.70915687   24.0069880  49.411326 0.0000000
## M058_S_R-M058_C_L      39.40103666   26.6988678  52.103205 0.0000000
## M058_S_S-M058_C_L      89.49519361   76.7930248 102.197362 0.0000000
## M248_C_L-M058_C_L       0.82420977  -11.8779591  13.526379 1.0000000
## M248_C_R-M058_C_L       0.68180418  -12.0203646  13.383973 1.0000000
## M248_C_S-M058_C_L       2.97761098   -9.7245578  15.679780 0.9999958
## M248_S_L-M058_C_L      54.30899570   41.6068269  67.011165 0.0000000
## M248_S_R-M058_C_L      41.44869285   28.7465240  54.150862 0.0000000
## M248_S_S-M058_C_L     102.99343687   90.2912680 115.695606 0.0000000
## M058_C_S-M058_C_R       2.53290662  -10.1692622  15.235075 0.9999996
## M058_S_L-M058_C_R      36.74776774   24.0455989  49.449937 0.0000000
## M058_S_R-M058_C_R      39.43964753   26.7374787  52.141816 0.0000000
## M058_S_S-M058_C_R      89.53380448   76.8316357 102.235973 0.0000000
## M248_C_L-M058_C_R       0.86282065  -11.8393482  13.564989 1.0000000
## M248_C_R-M058_C_R       0.72041505  -11.9817538  13.422584 1.0000000
## M248_C_S-M058_C_R       3.01622186   -9.6859470  15.718391 0.9999949
## M248_S_L-M058_C_R      54.34760657   41.6454377  67.049775 0.0000000
## M248_S_R-M058_C_R      41.48730372   28.7851349  54.189473 0.0000000
## M248_S_S-M058_C_R     103.03204774   90.3298789 115.734217 0.0000000
## M058_S_L-M058_C_S      34.21486112   21.5126923  46.917030 0.0000000
## M058_S_R-M058_C_S      36.90674091   24.2045721  49.608910 0.0000000
## M058_S_S-M058_C_S      87.00089786   74.2987290  99.703067 0.0000000
## M248_C_L-M058_C_S      -1.67008598  -14.3722548  11.032083 1.0000000
## M248_C_R-M058_C_S      -1.81249157  -14.5146604  10.889677 1.0000000
## M248_C_S-M058_C_S       0.48331523  -12.2188536  13.185484 1.0000000
## M248_S_L-M058_C_S      51.81469995   39.1125311  64.516869 0.0000000
## M248_S_R-M058_C_S      38.95439710   26.2522283  51.656566 0.0000000
## M248_S_S-M058_C_S     100.49914112   87.7969723 113.201310 0.0000000
## M058_S_R-M058_S_L       2.69187979  -10.0102890  15.394049 0.9999991
## M058_S_S-M058_S_L      52.78603674   40.0838679  65.488206 0.0000000
## M248_C_L-M058_S_L     -35.88494710  -48.5871159 -23.182778 0.0000000
## M248_C_R-M058_S_L     -36.02735269  -48.7295215 -23.325184 0.0000000
## M248_C_S-M058_S_L     -33.73154589  -46.4337147 -21.029377 0.0000000
## M248_S_L-M058_S_L      17.59983883    4.8976700  30.302008 0.0002648
## M248_S_R-M058_S_L       4.73953598   -7.9626328  17.441705 0.9977106
## M248_S_S-M058_S_L      66.28428000   53.5821112  78.986449 0.0000000
## M058_S_S-M058_S_R      50.09415695   37.3919881  62.796326 0.0000000
## M248_C_L-M058_S_R     -38.57682689  -51.2789957 -25.874658 0.0000000
## M248_C_R-M058_S_R     -38.71923248  -51.4214013 -26.017064 0.0000000
## M248_C_S-M058_S_R     -36.42342568  -49.1255945 -23.721257 0.0000000
## M248_S_L-M058_S_R      14.90795904    2.2057902  27.610128 0.0059976
## M248_S_R-M058_S_R       2.04765619  -10.6545126  14.749825 1.0000000
## M248_S_S-M058_S_R      63.59240021   50.8902314  76.294569 0.0000000
## M248_C_L-M058_S_S     -88.67098384 -101.3731527 -75.968815 0.0000000
## M248_C_R-M058_S_S     -88.81338943 -101.5155583 -76.111221 0.0000000
## M248_C_S-M058_S_S     -86.51758263  -99.2197515 -73.815414 0.0000000
## M248_S_L-M058_S_S     -35.18619791  -47.8883667 -22.484029 0.0000000
## M248_S_R-M058_S_S     -48.04650076  -60.7486696 -35.344332 0.0000000
## M248_S_S-M058_S_S      13.49824326    0.7960744  26.200412 0.0244897
## M248_C_R-M248_C_L      -0.14240560  -12.8445744  12.559763 1.0000000
## M248_C_S-M248_C_L       2.15340121  -10.5487676  14.855570 1.0000000
## M248_S_L-M248_C_L      53.48478593   40.7826171  66.186955 0.0000000
## M248_S_R-M248_C_L      40.62448308   27.9223143  53.326652 0.0000000
## M248_S_S-M248_C_L     102.16922709   89.4670583 114.871396 0.0000000
## M248_C_S-M248_C_R       2.29580680  -10.4063620  14.997976 0.9999999
## M248_S_L-M248_C_R      53.62719152   40.9250227  66.329360 0.0000000
## M248_S_R-M248_C_R      40.76688867   28.0647198  53.469057 0.0000000
## M248_S_S-M248_C_R     102.31163269   89.6094639 115.013802 0.0000000
## M248_S_L-M248_C_S      51.33138472   38.6292159  64.033554 0.0000000
## M248_S_R-M248_C_S      38.47108187   25.7689130  51.173251 0.0000000
## M248_S_S-M248_C_S     100.01582588   87.3136571 112.717995 0.0000000
## M248_S_R-M248_S_L     -12.86030285  -25.5624717  -0.158134 0.0436072
## M248_S_S-M248_S_L      48.68444117   35.9822723  61.386610 0.0000000
## M248_S_S-M248_S_R      61.54474402   48.8425752  74.246913 0.0000000
P9 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P9)
stat.test
## LA1511_C_R LA1511_C_S LA1511_S_L LA1511_S_R LA1511_S_S   M058_C_L   M058_C_R 
##        "a"        "a"        "b"        "b"        "c"        "a"        "a" 
##   M058_C_S   M058_S_L   M058_S_R   M058_S_S   M248_C_L   M248_C_R   M248_C_S 
##        "a"        "b"        "b"        "d"        "a"        "a"        "a" 
##   M248_S_L   M248_S_R   M248_S_S LA1511_C_L 
##        "e"        "b"        "f"        "a"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
ICP$Tissue <- factor(ICP$Tissue, levels = c("L", "S", "R"))


Na_content <- ggplot(data = ICP, mapping = aes(x = All.ID, y = Na.con.mg.mg.dry.weight, colour = Condition)) 
Na_content <- Na_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Na_content <- Na_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Na_content <- Na_content + scale_color_manual(values = c("blue","red"))
Na_content <- Na_content + ylab("Na content, mg/mg dry weight") + xlab("") #+ ggtitle("")
Na_content <- Na_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Na_content <- Na_content + stat_pvalue_manual(test, label = "Tukey", y.position = 150)
Na_content

Na_content <- ggplot(data = ICP, mapping = aes(x = Condition, y = Na.con.mg.mg.dry.weight, colour = Condition)) 
Na_content <- Na_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Na_content <- Na_content + facet_grid(Tissue ~ Accession)
Na_content <- Na_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Na_content <- Na_content + scale_color_manual(values = c("blue","red"))
Na_content <- Na_content + ylab("Na content, mg/mg dry weight") + xlab("")
Na_content <- Na_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Na_content <- Na_content + rremove("legend")
Na_content

Na_content <- ggplot(data = ICP, mapping = aes(x = Tissue, y = Na.con.mg.mg.dry.weight, colour = Condition)) 
Na_content <- Na_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Na_content <- Na_content + facet_grid(Condition ~ Accession)
Na_content <- Na_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Na_content <- Na_content + scale_color_manual(values = c("blue","red"))
Na_content <- Na_content + ylab("Na content, mg/mg dry weight") + xlab("")
Na_content <- Na_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Na_content <- Na_content + rremove("legend")
Na_content

Na_content <- ggplot(data = ICP, mapping = aes(x = Accession, y = Na.con.mg.mg.dry.weight, colour = Condition)) 
Na_content <- Na_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
Na_content <- Na_content + facet_grid(Condition ~ Tissue)
Na_content <- Na_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
Na_content <- Na_content + scale_color_manual(values = c("blue","red"))
Na_content <- Na_content + ylab("Na content, mg/mg dry weight") + xlab("")
Na_content <- Na_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
Na_content <- Na_content + rremove("legend")
Na_content

aov(K.con..mg.mg.dry.weight ~ All.ID, data = ICP)
## Call:
##    aov(formula = K.con..mg.mg.dry.weight ~ All.ID, data = ICP)
## 
## Terms:
##                    All.ID Residuals
## Sum of Squares  299308.12  57248.52
## Deg. of Freedom        17       240
## 
## Residual standard error: 15.44459
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(K.con..mg.mg.dry.weight ~ All.ID, data = ICP))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = K.con..mg.mg.dry.weight ~ All.ID, data = ICP)
## 
## $All.ID
##                               diff         lwr         upr     p adj
## LA1511_C_R-LA1511_C_L   27.1733169    5.804954  48.5416800 0.0015122
## LA1511_C_S-LA1511_C_L   68.2161069   46.847744  89.5844699 0.0000000
## LA1511_S_L-LA1511_C_L  -16.9970909  -38.365454   4.3712721 0.3165340
## LA1511_S_R-LA1511_C_L   -2.7674902  -24.135853  18.6008729 1.0000000
## LA1511_S_S-LA1511_C_L   10.3291329  -11.039230  31.6974960 0.9640016
## M058_C_L-LA1511_C_L      1.8854339  -18.758366  22.5292338 1.0000000
## M058_C_R-LA1511_C_L     28.7669697    8.123170  49.4107697 0.0002333
## M058_C_S-LA1511_C_L     95.2409643   74.597164 115.8847643 0.0000000
## M058_S_L-LA1511_C_L    -24.5712108  -45.215011  -3.9274108 0.0047902
## M058_S_R-LA1511_C_L     -1.4976554  -22.141455  19.1461446 1.0000000
## M058_S_S-LA1511_C_L    -18.3548887  -38.998689   2.2889112 0.1502011
## M248_C_L-LA1511_C_L      2.5718172  -18.071983  23.2156172 1.0000000
## M248_C_R-LA1511_C_L     14.0676534   -6.576147  34.7114533 0.6057841
## M248_C_S-LA1511_C_L     77.2001131   56.556313  97.8439130 0.0000000
## M248_S_L-LA1511_C_L    -21.9299732  -42.573773  -1.2861732 0.0245973
## M248_S_R-LA1511_C_L     -0.8760233  -21.519823  19.7677767 1.0000000
## M248_S_S-LA1511_C_L    -11.6714824  -32.315282   8.9723176 0.8691940
## LA1511_C_S-LA1511_C_R   41.0427900   19.674427  62.4111530 0.0000000
## LA1511_S_L-LA1511_C_R  -44.1704079  -65.538771 -22.8020448 0.0000000
## LA1511_S_R-LA1511_C_R  -29.9408071  -51.309170  -8.5724441 0.0002063
## LA1511_S_S-LA1511_C_R  -16.8441840  -38.212547   4.5241791 0.3325433
## M058_C_L-LA1511_C_R    -25.2878831  -45.931683  -4.6440831 0.0029591
## M058_C_R-LA1511_C_R      1.5936528  -19.050147  22.2374528 1.0000000
## M058_C_S-LA1511_C_R     68.0676474   47.423847  88.7114473 0.0000000
## M058_S_L-LA1511_C_R    -51.7445277  -72.388328 -31.1007278 0.0000000
## M058_S_R-LA1511_C_R    -28.6709723  -49.314772  -8.0271724 0.0002513
## M058_S_S-LA1511_C_R    -45.5282057  -66.172006 -24.8844057 0.0000000
## M248_C_L-LA1511_C_R    -24.6014997  -45.245300  -3.9576997 0.0046951
## M248_C_R-LA1511_C_R    -13.1056636  -33.749464   7.5381364 0.7252190
## M248_C_S-LA1511_C_R     50.0267961   29.382996  70.6705961 0.0000000
## M248_S_L-LA1511_C_R    -49.1032901  -69.747090 -28.4594902 0.0000000
## M248_S_R-LA1511_C_R    -28.0493402  -48.693140  -7.4055403 0.0004043
## M248_S_S-LA1511_C_R    -38.8447993  -59.488599 -18.2009993 0.0000000
## LA1511_S_L-LA1511_C_S  -85.2131978 -106.581561 -63.8448348 0.0000000
## LA1511_S_R-LA1511_C_S  -70.9835971  -92.351960 -49.6152340 0.0000000
## LA1511_S_S-LA1511_C_S  -57.8869739  -79.255337 -36.5186109 0.0000000
## M058_C_L-LA1511_C_S    -66.3306730  -86.974473 -45.6868731 0.0000000
## M058_C_R-LA1511_C_S    -39.4491372  -60.092937 -18.8053372 0.0000000
## M058_C_S-LA1511_C_S     27.0248574    6.381057  47.6686574 0.0008666
## M058_S_L-LA1511_C_S    -92.7873177 -113.431118 -72.1435177 0.0000000
## M058_S_R-LA1511_C_S    -69.7137623  -90.357562 -49.0699623 0.0000000
## M058_S_S-LA1511_C_S    -86.5709956 -107.214796 -65.9271957 0.0000000
## M248_C_L-LA1511_C_S    -65.6442897  -86.288090 -45.0004897 0.0000000
## M248_C_R-LA1511_C_S    -54.1484535  -74.792253 -33.5046536 0.0000000
## M248_C_S-LA1511_C_S      8.9840062  -11.659794  29.6278061 0.9871833
## M248_S_L-LA1511_C_S    -90.1460801 -110.789880 -69.5022801 0.0000000
## M248_S_R-LA1511_C_S    -69.0921302  -89.735930 -48.4483302 0.0000000
## M248_S_S-LA1511_C_S    -79.8875893 -100.531389 -59.2437893 0.0000000
## LA1511_S_R-LA1511_S_L   14.2296007   -7.138762  35.5979638 0.6467476
## LA1511_S_S-LA1511_S_L   27.3262239    5.957861  48.6945869 0.0013612
## M058_C_L-LA1511_S_L     18.8825248   -1.761275  39.5263247 0.1188905
## M058_C_R-LA1511_S_L     45.7640606   25.120261  66.4078606 0.0000000
## M058_C_S-LA1511_S_L    112.2380552   91.594255 132.8818552 0.0000000
## M058_S_L-LA1511_S_L     -7.5741199  -28.217920  13.0696801 0.9981294
## M058_S_R-LA1511_S_L     15.4994355   -5.144364  36.1432355 0.4226951
## M058_S_S-LA1511_S_L     -1.3577978  -22.001598  19.2860021 1.0000000
## M248_C_L-LA1511_S_L     19.5689082   -1.074892  40.2127081 0.0861348
## M248_C_R-LA1511_S_L     31.0647443   10.420944  51.7085443 0.0000370
## M248_C_S-LA1511_S_L     94.1972040   73.553404 114.8410040 0.0000000
## M248_S_L-LA1511_S_L     -4.9328823  -25.576682  15.7109177 0.9999944
## M248_S_R-LA1511_S_L     16.1210676   -4.522732  36.7648676 0.3494476
## M248_S_S-LA1511_S_L      5.3256085  -15.318191  25.9694085 0.9999829
## LA1511_S_S-LA1511_S_R   13.0966231   -8.271740  34.4649862 0.7762704
## M058_C_L-LA1511_S_R      4.6529241  -15.990876  25.2967240 0.9999977
## M058_C_R-LA1511_S_R     31.5344599   10.890660  52.1782599 0.0000250
## M058_C_S-LA1511_S_R     98.0084545   77.364655 118.6522545 0.0000000
## M058_S_L-LA1511_S_R    -21.8037206  -42.447521  -1.1599207 0.0264421
## M058_S_R-LA1511_S_R      1.2698348  -19.373965  21.9136347 1.0000000
## M058_S_S-LA1511_S_R    -15.5873986  -36.231199   5.0564014 0.4119733
## M248_C_L-LA1511_S_R      5.3393074  -15.304493  25.9831074 0.9999823
## M248_C_R-LA1511_S_R     16.8351436   -3.808656  37.4789435 0.2739931
## M248_C_S-LA1511_S_R     79.9676033   59.323803 100.6114032 0.0000000
## M248_S_L-LA1511_S_R    -19.1624830  -39.806283   1.4813170 0.1044999
## M248_S_R-LA1511_S_R      1.8914669  -18.752333  22.5352669 1.0000000
## M248_S_S-LA1511_S_R     -8.9039922  -29.547792  11.7398078 0.9883290
## M058_C_L-LA1511_S_S     -8.4436991  -29.087499  12.2001009 0.9934181
## M058_C_R-LA1511_S_S     18.4378368   -2.205963  39.0816367 0.1449010
## M058_C_S-LA1511_S_S     84.9118314   64.268031 105.5556313 0.0000000
## M058_S_L-LA1511_S_S    -34.9003438  -55.544144 -14.2565438 0.0000013
## M058_S_R-LA1511_S_S    -11.8267884  -32.470588   8.8170116 0.8562932
## M058_S_S-LA1511_S_S    -28.6840217  -49.327822  -8.0402217 0.0002488
## M248_C_L-LA1511_S_S     -7.7573157  -28.401116  12.8864843 0.9975103
## M248_C_R-LA1511_S_S      3.7385204  -16.905280  24.3823204 0.9999999
## M248_C_S-LA1511_S_S     66.8709801   46.227180  87.5147801 0.0000000
## M248_S_L-LA1511_S_S    -32.2591061  -52.902906 -11.6153062 0.0000135
## M248_S_R-LA1511_S_S    -11.2051562  -31.848956   9.4386437 0.9035825
## M248_S_S-LA1511_S_S    -22.0006153  -42.644415  -1.3568154 0.0236160
## M058_C_R-M058_C_L       26.8815359    6.988672  46.7743993 0.0004539
## M058_C_S-M058_C_L       93.3555305   73.462667 113.2483939 0.0000000
## M058_S_L-M058_C_L      -26.4566447  -46.349508  -6.5637813 0.0006311
## M058_S_R-M058_C_L       -3.3830893  -23.275953  16.5097741 1.0000000
## M058_S_S-M058_C_L      -20.2403226  -40.133186  -0.3474592 0.0412387
## M248_C_L-M058_C_L        0.6863834  -19.206480  20.5792468 1.0000000
## M248_C_R-M058_C_L       12.1822195   -7.710644  32.0750829 0.7773945
## M248_C_S-M058_C_L       75.3146792   55.421816  95.2075426 0.0000000
## M248_S_L-M058_C_L      -23.8154070  -43.708270  -3.9225436 0.0043559
## M248_S_R-M058_C_L       -2.7614572  -22.654321  17.1314062 1.0000000
## M248_S_S-M058_C_L      -13.5569162  -33.449780   6.3359472 0.6056522
## M058_C_S-M058_C_R       66.4739946   46.581131  86.3668580 0.0000000
## M058_S_L-M058_C_R      -53.3381805  -73.231044 -33.4453171 0.0000000
## M058_S_R-M058_C_R      -30.2646251  -50.157489 -10.3717617 0.0000278
## M058_S_S-M058_C_R      -47.1218585  -67.014722 -27.2289951 0.0000000
## M248_C_L-M058_C_R      -26.1951525  -46.088016  -6.3022891 0.0007712
## M248_C_R-M058_C_R      -14.6993164  -34.592180   5.1935470 0.4530977
## M248_C_S-M058_C_R       48.4331434   28.540280  68.3260068 0.0000000
## M248_S_L-M058_C_R      -50.6969429  -70.589806 -30.8040795 0.0000000
## M248_S_R-M058_C_R      -29.6429930  -49.535856  -9.7501296 0.0000474
## M248_S_S-M058_C_R      -40.4384521  -60.331315 -20.5455887 0.0000000
## M058_S_L-M058_C_S     -119.8121751 -139.705039 -99.9193117 0.0000000
## M058_S_R-M058_C_S      -96.7386197 -116.631483 -76.8457563 0.0000000
## M058_S_S-M058_C_S     -113.5958531 -133.488716 -93.7029897 0.0000000
## M248_C_L-M058_C_S      -92.6691471 -112.562010 -72.7762837 0.0000000
## M248_C_R-M058_C_S      -81.1733109 -101.066174 -61.2804475 0.0000000
## M248_C_S-M058_C_S      -18.0408512  -37.933715   1.8520122 0.1278286
## M248_S_L-M058_C_S     -117.1709375 -137.063801 -97.2780741 0.0000000
## M248_S_R-M058_C_S      -96.1169876 -116.009851 -76.2241242 0.0000000
## M248_S_S-M058_C_S     -106.9124467 -126.805310 -87.0195833 0.0000000
## M058_S_R-M058_S_L       23.0735554    3.180692  42.9664188 0.0072072
## M058_S_S-M058_S_L        6.2163221  -13.676541  26.1091855 0.9997564
## M248_C_L-M058_S_L       27.1430280    7.250165  47.0358914 0.0003696
## M248_C_R-M058_S_L       38.6388642   18.746001  58.5317276 0.0000000
## M248_C_S-M058_S_L      101.7713239   81.878460 121.6641873 0.0000000
## M248_S_L-M058_S_L        2.6412376  -17.251626  22.5341010 1.0000000
## M248_S_R-M058_S_L       23.6951875    3.802324  43.5880509 0.0047321
## M248_S_S-M058_S_L       12.8997284   -6.993135  32.7925918 0.6915751
## M058_S_S-M058_S_R      -16.8572333  -36.750097   3.0356301 0.2140527
## M248_C_L-M058_S_R        4.0694726  -15.823391  23.9623361 0.9999995
## M248_C_R-M058_S_R       15.5653088   -4.327555  35.4581722 0.3458727
## M248_C_S-M058_S_R       78.6977685   58.804905  98.5906319 0.0000000
## M248_S_L-M058_S_R      -20.4323178  -40.325181  -0.5394544 0.0369961
## M248_S_R-M058_S_R        0.6216321  -19.271231  20.5144955 1.0000000
## M248_S_S-M058_S_R      -10.1738270  -30.066690   9.7190364 0.9406068
## M248_C_L-M058_S_S       20.9267060    1.033843  40.8195694 0.0277848
## M248_C_R-M058_S_S       32.4225421   12.529679  52.3154055 0.0000041
## M248_C_S-M058_S_S       95.5550018   75.662138 115.4478652 0.0000000
## M248_S_L-M058_S_S       -3.5750844  -23.467948  16.3177790 0.9999999
## M248_S_R-M058_S_S       17.4788654   -2.413998  37.3717289 0.1647031
## M248_S_S-M058_S_S        6.6834064  -13.209457  26.5762698 0.9993737
## M248_C_R-M248_C_L       11.4958361   -8.397027  31.3886995 0.8473448
## M248_C_S-M248_C_L       74.6282958   54.735432  94.5211592 0.0000000
## M248_S_L-M248_C_L      -24.5017904  -44.394654  -4.6089270 0.0026908
## M248_S_R-M248_C_L       -3.4478405  -23.340704  16.4450229 1.0000000
## M248_S_S-M248_C_L      -14.2432996  -34.136163   5.6495638 0.5133905
## M248_C_S-M248_C_R       63.1324597   43.239596  83.0253231 0.0000000
## M248_S_L-M248_C_R      -35.9976266  -55.890490 -16.1047632 0.0000001
## M248_S_R-M248_C_R      -14.9436767  -34.836540   4.9491867 0.4216728
## M248_S_S-M248_C_R      -25.7391357  -45.631999  -5.8462723 0.0010887
## M248_S_L-M248_C_S      -99.1300863 -119.022950 -79.2372229 0.0000000
## M248_S_R-M248_C_S      -78.0761364  -97.969000 -58.1832730 0.0000000
## M248_S_S-M248_C_S      -88.8715954 -108.764459 -68.9787320 0.0000000
## M248_S_R-M248_S_L       21.0539499    1.161086  40.9468133 0.0257709
## M248_S_S-M248_S_L       10.2584908   -9.634373  30.1513542 0.9362862
## M248_S_S-M248_S_R      -10.7954591  -30.688322   9.0974043 0.9037278
P8 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P8)
stat.test
## LA1511_C_R LA1511_C_S LA1511_S_L LA1511_S_R LA1511_S_S   M058_C_L   M058_C_R 
##        "a"        "b"     "cdef"     "cdeg"       "ag"       "cg"        "a" 
##   M058_C_S   M058_S_L   M058_S_R   M058_S_S   M248_C_L   M248_C_R   M248_C_S 
##        "h"        "f"      "cdg"      "def"       "cg"       "ag"       "bh" 
##   M248_S_L   M248_S_R   M248_S_S LA1511_C_L 
##       "ef"      "cdg"     "cdef"      "cdg"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
K_content <- ggplot(data = ICP, mapping = aes(x = All.ID, y = K.con..mg.mg.dry.weight, colour = Condition)) 
K_content <- K_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
K_content <- K_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
K_content <- K_content + scale_color_manual(values = c("blue","red"))
K_content <- K_content + ylab("K content, mg/mg dry weight") + xlab("")
K_content <- K_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
K_content <- K_content + stat_pvalue_manual(test, label = "Tukey", y.position = 80)
K_content

k_content <- ggplot(data = ICP, mapping = aes(x = Condition, y = K.con..mg.mg.dry.weight, colour = Condition)) 
k_content <- k_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
k_content <- k_content + facet_grid(Tissue ~ Accession)
k_content <- k_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
k_content <- k_content + scale_color_manual(values = c("blue","red"))
k_content <- k_content + ylab("K content, mg/mg dry weight") + xlab("")
k_content <- k_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
k_content <- k_content + rremove("legend")
k_content

k_content <- ggplot(data = ICP, mapping = aes(x = Tissue, y = K.con..mg.mg.dry.weight, colour = Condition)) 
k_content <- k_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
k_content <- k_content + facet_grid(Condition ~ Accession)
k_content <- k_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
k_content <- k_content + scale_color_manual(values = c("blue","red"))
k_content <- k_content + ylab("K content, mg/mg dry weight") + xlab("")
k_content <- k_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
k_content <- k_content + rremove("legend")
k_content

k_content <- ggplot(data = ICP, mapping = aes(x = Accession, y = K.con..mg.mg.dry.weight, colour = Condition)) 
k_content <- k_content + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
k_content <- k_content + facet_grid(Condition ~ Tissue)
k_content <- k_content + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
k_content <- k_content + scale_color_manual(values = c("blue","red"))
k_content <- k_content + ylab("K content, mg/mg dry weight") + xlab("")
k_content <- k_content + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
k_content <- k_content + rremove("legend")
k_content

aov(DW.mg ~ All.ID, data = ICP)
## Call:
##    aov(formula = DW.mg ~ All.ID, data = ICP)
## 
## Terms:
##                    All.ID Residuals
## Sum of Squares  11031.735  6450.923
## Deg. of Freedom        17       240
## 
## Residual standard error: 5.184481
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(DW.mg ~ All.ID, data = ICP))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = DW.mg ~ All.ID, data = ICP)
## 
## $All.ID
##                               diff          lwr          upr     p adj
## LA1511_C_R-LA1511_C_L -15.45384615 -22.62683293  -8.28085937 0.0000000
## LA1511_C_S-LA1511_C_L -12.65384615 -19.82683293  -5.48085937 0.0000003
## LA1511_S_L-LA1511_C_L  -7.25384615 -14.42683293  -0.08085937 0.0441794
## LA1511_S_R-LA1511_C_L -18.86153846 -26.03452524 -11.68855168 0.0000000
## LA1511_S_S-LA1511_C_L -17.26923077 -24.44221755 -10.09624399 0.0000000
## M058_C_L-LA1511_C_L    -8.86461538 -15.79437897  -1.93485180 0.0013534
## M058_C_R-LA1511_C_L   -19.28461538 -26.21437897 -12.35485180 0.0000000
## M058_C_S-LA1511_C_L   -17.32461538 -24.25437897 -10.39485180 0.0000000
## M058_S_L-LA1511_C_L   -15.93128205 -22.86104564  -9.00151846 0.0000000
## M058_S_R-LA1511_C_L   -20.71128205 -27.64104564 -13.78151846 0.0000000
## M058_S_S-LA1511_C_L   -21.52461538 -28.45437897 -14.59485180 0.0000000
## M248_C_L-LA1511_C_L     0.29538462  -6.63437897   7.22514820 1.0000000
## M248_C_R-LA1511_C_L   -14.65128205 -21.58104564  -7.72151846 0.0000000
## M248_C_S-LA1511_C_L    -8.58461538 -15.51437897  -1.65485180 0.0024319
## M248_S_L-LA1511_C_L   -11.07128205 -18.00104564  -4.14151846 0.0000073
## M248_S_R-LA1511_C_L   -20.32461538 -27.25437897 -13.39485180 0.0000000
## M248_S_S-LA1511_C_L   -20.29128205 -27.22104564 -13.36151846 0.0000000
## LA1511_C_S-LA1511_C_R   2.80000000  -4.37298678   9.97298678 0.9961152
## LA1511_S_L-LA1511_C_R   8.20000000   1.02701322  15.37298678 0.0089780
## LA1511_S_R-LA1511_C_R  -3.40769231 -10.58067909   3.76529447 0.9693783
## LA1511_S_S-LA1511_C_R  -1.81538462  -8.98837139   5.35760216 0.9999871
## M058_C_L-LA1511_C_R     6.58923077  -0.34053282  13.51899436 0.0836446
## M058_C_R-LA1511_C_R    -3.83076923 -10.76053282   3.09899436 0.8891468
## M058_C_S-LA1511_C_R    -1.87076923  -8.80053282   5.05899436 0.9999674
## M058_S_L-LA1511_C_R    -0.47743590  -7.40719949   6.45232769 1.0000000
## M058_S_R-LA1511_C_R    -5.25743590 -12.18719949   1.67232769 0.4029730
## M058_S_S-LA1511_C_R    -6.07076923 -13.00053282   0.85899436 0.1684696
## M248_C_L-LA1511_C_R    15.74923077   8.81946718  22.67899436 0.0000000
## M248_C_R-LA1511_C_R     0.80256410  -6.12719949   7.73232769 1.0000000
## M248_C_S-LA1511_C_R     6.86923077  -0.06053282  13.79899436 0.0549534
## M248_S_L-LA1511_C_R     4.38256410  -2.54719949  11.31232769 0.7310576
## M248_S_R-LA1511_C_R    -4.87076923 -11.80053282   2.05899436 0.5484674
## M248_S_S-LA1511_C_R    -4.83743590 -11.76719949   2.09232769 0.5613578
## LA1511_S_L-LA1511_C_S   5.40000000  -1.77298678  12.57298678 0.4175966
## LA1511_S_R-LA1511_C_S  -6.20769231 -13.38067909   0.96529447 0.1844604
## LA1511_S_S-LA1511_C_S  -4.61538462 -11.78837139   2.55760216 0.7041356
## M058_C_L-LA1511_C_S     3.78923077  -3.14053282  10.71899436 0.8979426
## M058_C_R-LA1511_C_S    -6.63076923 -13.56053282   0.29899436 0.0787315
## M058_C_S-LA1511_C_S    -4.67076923 -11.60053282   2.25899436 0.6254844
## M058_S_L-LA1511_C_S    -3.27743590 -10.20719949   3.65232769 0.9706478
## M058_S_R-LA1511_C_S    -8.05743590 -14.98719949  -1.12767231 0.0069407
## M058_S_S-LA1511_C_S    -8.87076923 -15.80053282  -1.94100564 0.0013358
## M248_C_L-LA1511_C_S    12.94923077   6.01946718  19.87899436 0.0000000
## M248_C_R-LA1511_C_S    -1.99743590  -8.92719949   4.93232769 0.9999185
## M248_C_S-LA1511_C_S     4.06923077  -2.86053282  10.99899436 0.8298042
## M248_S_L-LA1511_C_S     1.58256410  -5.34719949   8.51232769 0.9999971
## M248_S_R-LA1511_C_S    -7.67076923 -14.60053282  -0.74100564 0.0142687
## M248_S_S-LA1511_C_S    -7.63743590 -14.56719949  -0.70767231 0.0151524
## LA1511_S_R-LA1511_S_L -11.60769231 -18.78067909  -4.43470553 0.0000050
## LA1511_S_S-LA1511_S_L -10.01538462 -17.18837139  -2.84239784 0.0002232
## M058_C_L-LA1511_S_L    -1.61076923  -8.54053282   5.31899436 0.9999963
## M058_C_R-LA1511_S_L   -12.03076923 -18.96053282  -5.10100564 0.0000006
## M058_C_S-LA1511_S_L   -10.07076923 -17.00053282  -3.14100564 0.0000881
## M058_S_L-LA1511_S_L    -8.67743590 -15.60719949  -1.74767231 0.0020068
## M058_S_R-LA1511_S_L   -13.45743590 -20.38719949  -6.52767231 0.0000000
## M058_S_S-LA1511_S_L   -14.27076923 -21.20053282  -7.34100564 0.0000000
## M248_C_L-LA1511_S_L     7.54923077   0.61946718  14.47899436 0.0177355
## M248_C_R-LA1511_S_L    -7.39743590 -14.32719949  -0.46767231 0.0231244
## M248_C_S-LA1511_S_L    -1.33076923  -8.26053282   5.59899436 0.9999998
## M248_S_L-LA1511_S_L    -3.81743590 -10.74719949   3.11232769 0.8920205
## M248_S_R-LA1511_S_L   -13.07076923 -20.00053282  -6.14100564 0.0000000
## M248_S_S-LA1511_S_L   -13.03743590 -19.96719949  -6.10767231 0.0000000
## LA1511_S_S-LA1511_S_R   1.59230769  -5.58067909   8.76529447 0.9999981
## M058_C_L-LA1511_S_R     9.99692308   3.06715949  16.92668666 0.0001051
## M058_C_R-LA1511_S_R    -0.42307692  -7.35284051   6.50668666 1.0000000
## M058_C_S-LA1511_S_R     1.53692308  -5.39284051   8.46668666 0.9999982
## M058_S_L-LA1511_S_R     2.93025641  -3.99950718   9.86002000 0.9905443
## M058_S_R-LA1511_S_R    -1.84974359  -8.77950718   5.08002000 0.9999722
## M058_S_S-LA1511_S_R    -2.66307692  -9.59284051   4.26668666 0.9967589
## M248_C_L-LA1511_S_R    19.15692308  12.22715949  26.08668666 0.0000000
## M248_C_R-LA1511_S_R     4.21025641  -2.71950718  11.14002000 0.7879850
## M248_C_S-LA1511_S_R    10.27692308   3.34715949  17.20668666 0.0000535
## M248_S_L-LA1511_S_R     7.79025641   0.86049282  14.72002000 0.0114726
## M248_S_R-LA1511_S_R    -1.46307692  -8.39284051   5.46668666 0.9999991
## M248_S_S-LA1511_S_R    -1.42974359  -8.35950718   5.50002000 0.9999994
## M058_C_L-LA1511_S_S     8.40461538   1.47485180  15.33437897 0.0035077
## M058_C_R-LA1511_S_S    -2.01538462  -8.94514820   4.91437897 0.9999078
## M058_C_S-LA1511_S_S    -0.05538462  -6.98514820   6.87437897 1.0000000
## M058_S_L-LA1511_S_S     1.33794872  -5.59181487   8.26771231 0.9999998
## M058_S_R-LA1511_S_S    -3.44205128 -10.37181487   3.48771231 0.9539503
## M058_S_S-LA1511_S_S    -4.25538462 -11.18514820   2.67437897 0.7736503
## M248_C_L-LA1511_S_S    17.56461538  10.63485180  24.49437897 0.0000000
## M248_C_R-LA1511_S_S     2.61794872  -4.31181487   9.54771231 0.9973478
## M248_C_S-LA1511_S_S     8.68461538   1.75485180  15.61437897 0.0019770
## M248_S_L-LA1511_S_S     6.19794872  -0.73181487  13.12771231 0.1432766
## M248_S_R-LA1511_S_S    -3.05538462  -9.98514820   3.87437897 0.9853300
## M248_S_S-LA1511_S_S    -3.02205128  -9.95181487   3.90771231 0.9869028
## M058_C_R-M058_C_L     -10.42000000 -17.09768728  -3.74231272 0.0000141
## M058_C_S-M058_C_L      -8.46000000 -15.13768728  -1.78231272 0.0016211
## M058_S_L-M058_C_L      -7.06666667 -13.74435395  -0.38897939 0.0258064
## M058_S_R-M058_C_L     -11.84666667 -18.52435395  -5.16897939 0.0000003
## M058_S_S-M058_C_L     -12.66000000 -19.33768728  -5.98231272 0.0000000
## M248_C_L-M058_C_L       9.16000000   2.48231272  15.83768728 0.0003297
## M248_C_R-M058_C_L      -5.78666667 -12.46435395   0.89102061 0.1826910
## M248_C_S-M058_C_L       0.28000000  -6.39768728   6.95768728 1.0000000
## M248_S_L-M058_C_L      -2.20666667  -8.88435395   4.47102061 0.9994936
## M248_S_R-M058_C_L     -11.46000000 -18.13768728  -4.78231272 0.0000008
## M248_S_S-M058_C_L     -11.42666667 -18.10435395  -4.74897939 0.0000009
## M058_C_S-M058_C_R       1.96000000  -4.71768728   8.63768728 0.9998954
## M058_S_L-M058_C_R       3.35333333  -3.32435395  10.03102061 0.9492827
## M058_S_R-M058_C_R      -1.42666667  -8.10435395   5.25102061 0.9999990
## M058_S_S-M058_C_R      -2.24000000  -8.91768728   4.43768728 0.9993861
## M248_C_L-M058_C_R      19.58000000  12.90231272  26.25768728 0.0000000
## M248_C_R-M058_C_R       4.63333333  -2.04435395  11.31102061 0.5726472
## M248_C_S-M058_C_R      10.70000000   4.02231272  17.37768728 0.0000067
## M248_S_L-M058_C_R       8.21333333   1.53564605  14.89102061 0.0027572
## M248_S_R-M058_C_R      -1.04000000  -7.71768728   5.63768728 1.0000000
## M248_S_S-M058_C_R      -1.00666667  -7.68435395   5.67102061 1.0000000
## M058_S_L-M058_C_S       1.39333333  -5.28435395   8.07102061 0.9999993
## M058_S_R-M058_C_S      -3.38666667 -10.06435395   3.29102061 0.9447283
## M058_S_S-M058_C_S      -4.20000000 -10.87768728   2.47768728 0.7393317
## M248_C_L-M058_C_S      17.62000000  10.94231272  24.29768728 0.0000000
## M248_C_R-M058_C_S       2.67333333  -4.00435395   9.35102061 0.9948200
## M248_C_S-M058_C_S       8.74000000   2.06231272  15.41768728 0.0008700
## M248_S_L-M058_C_S       6.25333333  -0.42435395  12.93102061 0.0964919
## M248_S_R-M058_C_S      -3.00000000  -9.67768728   3.67768728 0.9822443
## M248_S_S-M058_C_S      -2.96666667  -9.64435395   3.71102061 0.9841451
## M058_S_R-M058_S_L      -4.78000000 -11.45768728   1.89768728 0.5138799
## M058_S_S-M058_S_L      -5.59333333 -12.27102061   1.08435395 0.2314169
## M248_C_L-M058_S_L      16.22666667   9.54897939  22.90435395 0.0000000
## M248_C_R-M058_S_L       1.28000000  -5.39768728   7.95768728 0.9999998
## M248_C_S-M058_S_L       7.34666667   0.66897939  14.02435395 0.0155226
## M248_S_L-M058_S_L       4.86000000  -1.81768728  11.53768728 0.4821483
## M248_S_R-M058_S_L      -4.39333333 -11.07102061   2.28435395 0.6675043
## M248_S_S-M058_S_L      -4.36000000 -11.03768728   2.31768728 0.6802805
## M058_S_S-M058_S_R      -0.81333333  -7.49102061   5.86435395 1.0000000
## M248_C_L-M058_S_R      21.00666667  14.32897939  27.68435395 0.0000000
## M248_C_R-M058_S_R       6.06000000  -0.61768728  12.73768728 0.1271224
## M248_C_S-M058_S_R      12.12666667   5.44897939  18.80435395 0.0000001
## M248_S_L-M058_S_R       9.64000000   2.96231272  16.31768728 0.0001033
## M248_S_R-M058_S_R       0.38666667  -6.29102061   7.06435395 1.0000000
## M248_S_S-M058_S_R       0.42000000  -6.25768728   7.09768728 1.0000000
## M248_C_L-M058_S_S      21.82000000  15.14231272  28.49768728 0.0000000
## M248_C_R-M058_S_S       6.87333333   0.19564605  13.55102061 0.0360922
## M248_C_S-M058_S_S      12.94000000   6.26231272  19.61768728 0.0000000
## M248_S_L-M058_S_S      10.45333333   3.77564605  17.13102061 0.0000129
## M248_S_R-M058_S_S       1.20000000  -5.47768728   7.87768728 0.9999999
## M248_S_S-M058_S_S       1.23333333  -5.44435395   7.91102061 0.9999999
## M248_C_R-M248_C_L     -14.94666667 -21.62435395  -8.26897939 0.0000000
## M248_C_S-M248_C_L      -8.88000000 -15.55768728  -2.20231272 0.0006326
## M248_S_L-M248_C_L     -11.36666667 -18.04435395  -4.68897939 0.0000011
## M248_S_R-M248_C_L     -20.62000000 -27.29768728 -13.94231272 0.0000000
## M248_S_S-M248_C_L     -20.58666667 -27.26435395 -13.90897939 0.0000000
## M248_C_S-M248_C_R       6.06666667  -0.61102061  12.74435395 0.1259522
## M248_S_L-M248_C_R       3.58000000  -3.09768728  10.25768728 0.9124877
## M248_S_R-M248_C_R      -5.67333333 -12.35102061   1.00435395 0.2102843
## M248_S_S-M248_C_R      -5.64000000 -12.31768728   1.03768728 0.2189228
## M248_S_L-M248_C_S      -2.48666667  -9.16435395   4.19102061 0.9977645
## M248_S_R-M248_C_S     -11.74000000 -18.41768728  -5.06231272 0.0000004
## M248_S_S-M248_C_S     -11.70666667 -18.38435395  -5.02897939 0.0000004
## M248_S_R-M248_S_L      -9.25333333 -15.93102061  -2.57564605 0.0002642
## M248_S_S-M248_S_L      -9.22000000 -15.89768728  -2.54231272 0.0002860
## M248_S_S-M248_S_R       0.03333333  -6.64435395   6.71102061 1.0000000
P7 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P7)
stat.test
## LA1511_C_R LA1511_C_S LA1511_S_L LA1511_S_R LA1511_S_S   M058_C_L   M058_C_R 
##    "abcde"     "abcf"        "f"      "ade"     "abde"       "cf"      "ade" 
##   M058_C_S   M058_S_L   M058_S_R   M058_S_S   M248_C_L   M248_C_R   M248_C_S 
##     "abde"     "abde"       "de"        "d"        "g"     "abce"       "cf" 
##   M248_S_L   M248_S_R   M248_S_S LA1511_C_L 
##      "bcf"       "de"       "de"        "g"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
DW <- ggplot(data = ICP, mapping = aes(x = All.ID, y = DW.mg, colour = Condition)) 
DW <- DW + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

DW <- DW + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
DW <- DW + scale_color_manual(values = c("blue","red"))

DW <- DW + ylab("Dry weight, mg") + xlab("")
DW <- DW + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
DW <- DW + stat_pvalue_manual(test, label = "Tukey", y.position = 80)
DW

DW <- ggplot(data = ICP, mapping = aes(x = Condition, y = DW.mg, colour = Condition)) 
DW <- DW + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

DW <- DW + facet_grid(Tissue ~ Accession)
DW <- DW + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
DW <- DW + scale_color_manual(values = c("blue","red"))

DW <- DW + ylab("Dry weight, mg") + xlab("")
DW <- DW + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
DW <- DW + rremove("legend")
DW

DW <- ggplot(data = ICP, mapping = aes(x = Tissue, y = DW.mg, colour = Condition)) 
DW <- DW + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

DW <- DW + facet_grid(Condition ~ Accession)
DW <- DW + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
DW <- DW + scale_color_manual(values = c("blue","red"))

DW <- DW + ylab("Dry weight, mg") + xlab("")
DW <- DW + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
DW <- DW + rremove("legend")
DW

DW <- ggplot(data = ICP, mapping = aes(x = Accession, y = DW.mg, colour = Condition)) 
DW <- DW + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

DW <- DW + facet_grid(Condition ~ Tissue)
DW <- DW + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
DW <- DW + scale_color_manual(values = c("blue","red"))

DW <- DW + ylab("Dry weight, mg") + xlab("")
DW <- DW + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
DW <- DW + rremove("legend")
DW

FW<- read.csv("20220124_root_leaf_stem_separated_ICP_LA1511_M058_M248_freshWeight v2.csv")
FW
FW$All.ID <- paste(FW$ï..Genotype,FW$Condition,  sep="_")
FW
for(i in 1:nrow(FW)){
  FW$total.FW.g[i] <- sum(FW[i,3:5])  
}

FW
FW$total.FW.mg <- FW$total.FW.g * 1000
FW
aov(total.FW.mg ~ All.ID, data = FW)
## Call:
##    aov(formula = total.FW.mg ~ All.ID, data = FW)
## 
## Terms:
##                  All.ID Residuals
## Sum of Squares  7602071    639878
## Deg. of Freedom       5        80
## 
## Residual standard error: 89.43416
## Estimated effects may be unbalanced
## 2 observations deleted due to missingness
Output <- TukeyHSD(aov(total.FW.mg ~ All.ID, data = FW))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = total.FW.mg ~ All.ID, data = FW)
## 
## $All.ID
##                                   diff         lwr         upr     p adj
## LA1511_salt-LA1511_control  -404.71538 -507.143679 -302.287090 0.0000000
## M058_control-LA1511_control -281.95487 -380.910006 -182.999738 0.0000000
## M058_salt-LA1511_control    -605.36154 -704.316672 -506.406405 0.0000000
## M248_control-LA1511_control  241.93846  142.983328  340.893595 0.0000000
## M248_salt-LA1511_control    -501.61487 -600.570006 -402.659738 0.0000000
## M058_control-LA1511_salt     122.76051   23.805379  221.715647 0.0065580
## M058_salt-LA1511_salt       -200.64615 -299.601288 -101.691020 0.0000011
## M248_control-LA1511_salt     646.65385  547.698712  745.608980 0.0000000
## M248_salt-LA1511_salt        -96.89949 -195.854621    2.055647 0.0584220
## M058_salt-M058_control      -323.40667 -418.762220 -228.051114 0.0000000
## M248_control-M058_control    523.89333  428.537780  619.248886 0.0000000
## M248_salt-M058_control      -219.66000 -315.015553 -124.304447 0.0000000
## M248_control-M058_salt       847.30000  751.944447  942.655553 0.0000000
## M248_salt-M058_salt          103.74667    8.391114  199.102220 0.0249242
## M248_salt-M248_control      -743.55333 -838.908886 -648.197780 0.0000000
P8 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P8)
stat.test
##    LA1511_salt   M058_control      M058_salt   M248_control      M248_salt 
##            "a"            "b"            "c"            "d"            "a" 
## LA1511_control 
##            "e"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
unique(FW$Condition)
## [1] "salt"    "control" ""
FW <- na.omit(FW)
unique(FW$Condition)
## [1] "salt"    "control"
FW_graph <- ggplot(data = FW, mapping = aes(x = All.ID, y = total.FW.mg, colour = Condition)) 
FW_graph <- FW_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)
FW_graph <- FW_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
FW_graph <- FW_graph + scale_color_manual(values = c("blue","red"))
FW_graph <- FW_graph + ylab("Total fresh weight, mg") + xlab("") #+ ggtitle("")
FW_graph <- FW_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
FW_graph <- FW_graph + stat_pvalue_manual(test, label = "Tukey", y.position = 150)
FW_graph

FW_graph <- ggplot(data = FW, mapping = aes(x = Condition, y = total.FW.mg, colour = Condition)) 
FW_graph <- FW_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

FW_graph <- FW_graph + facet_grid(~ï..Genotype)
FW_graph <- FW_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
FW_graph <- FW_graph + scale_color_manual(values = c("blue","red"))

FW_graph <- FW_graph + ylab("Fresh weight, mg") + xlab("")
FW_graph <- FW_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
FW_graph <- FW_graph + rremove("legend")
FW_graph 

FW_graph <- ggplot(data = FW, mapping = aes(x = ï..Genotype, y = total.FW.mg, colour = Condition)) 
FW_graph <- FW_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

FW_graph <- FW_graph + facet_grid(~Condition)
FW_graph <- FW_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
FW_graph <- FW_graph + scale_color_manual(values = c("blue","red"))

FW_graph <- FW_graph + ylab("Fresh weight, mg") + xlab("")
FW_graph <- FW_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
FW_graph <- FW_graph + rremove("legend")
FW_graph

Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Ctrl+Alt+I.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Ctrl+Shift+K to preview the HTML file).

The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike Knit, Preview does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.