this is the shoot ion leakage experiment for the 5 Arabidopsis genotypes I did in soil.2 weeks old seedlings were subjected to 100 mM salt for 2 weeks. We measure Chl.Ind etc with CropReporter. Overall no difference in ion leakage between the genotypes as I expected based on my 2021 experiment. However, I did the RSA analysis for the same seedlings +/- in plate that I wait for those results to see whether I can replicate the duf story.

getwd()
## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20231020_ion_leakae_duf_wrky_2xko_soil_grown"
setwd("C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20231020_ion_leakae_duf_wrky_2xko_soil_grown/")
list.files(pattern = ".csv")
## [1] "20231019_duf_wrky_2xko_soil_salt_ion_leakage_forR.csv"
IL <- read.csv("20231019_duf_wrky_2xko_soil_salt_ion_leakage_forR.csv")
IL
IL$All.ID<-paste(IL$Geno, IL$Condition, IL$Tray,sep="_")
IL
library(ggplot2)
library(ggpubr)
library(multcompView)
aov(Ion.leakage ~ All.ID, data = IL)
## Call:
##    aov(formula = Ion.leakage ~ All.ID, data = IL)
## 
## Terms:
##                   All.ID Residuals
## Sum of Squares  25798.19  13139.54
## Deg. of Freedom       19       100
## 
## Residual standard error: 11.46278
## Estimated effects may be unbalanced
Output <- TukeyHSD(aov(Ion.leakage ~ All.ID, data = IL))
Output
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = Ion.leakage ~ All.ID, data = IL)
## 
## $All.ID
##                                 diff         lwr         upr     p adj
## 2xD_ctrl_B-2xD_ctrl_A    -1.27652146 -25.3716903  22.8186473 1.0000000
## 2xD_salt_A-2xD_ctrl_A    42.07256565  17.9773969  66.1677344 0.0000011
## 2xD_salt_B-2xD_ctrl_A    20.32486487  -3.7703039  44.4200337 0.2169692
## 2xE_ctrl_A-2xD_ctrl_A    -1.72602293 -25.8211917  22.3691459 1.0000000
## 2xE_ctrl_B-2xD_ctrl_A    -5.95323873 -30.0484075  18.1419301 0.9999951
## 2xE_salt_A-2xD_ctrl_A    24.85211270   0.7569439  48.9472815 0.0355323
## 2xE_salt_B-2xD_ctrl_A    19.09291959  -5.0022492  43.1880884 0.3179786
## col_ctrl_A-2xD_ctrl_A     5.50376005 -18.5914087  29.5989288 0.9999986
## col_ctrl_B-2xD_ctrl_A    -1.60357062 -25.6987394  22.4915982 1.0000000
## col_salt_A-2xD_ctrl_A    34.23601198  10.1408432  58.3311808 0.0002035
## col_salt_B-2xD_ctrl_A    15.34564334  -8.7495255  39.4408121 0.7170042
## duf_ctrl_A-2xD_ctrl_A    -2.38277599 -26.4779448  21.7123928 1.0000000
## duf_ctrl_B-2xD_ctrl_A    -5.69697209 -29.7921409  18.3981967 0.9999976
## duf_salt_A-2xD_ctrl_A    32.30860764   8.2134388  56.4037764 0.0006588
## duf_salt_B-2xD_ctrl_A    16.19887981  -7.8962890  40.2940486 0.6253071
## wrky_ctrl_A-2xD_ctrl_A    5.46035308 -18.6348157  29.5555219 0.9999988
## wrky_ctrl_B-2xD_ctrl_A   -1.94435066 -26.0395195  22.1508181 1.0000000
## wrky_salt_A-2xD_ctrl_A   27.23753174   3.1423629  51.3327005 0.0111138
## wrky_salt_B-2xD_ctrl_A   23.34065917  -0.7545096  47.4358280 0.0692754
## 2xD_salt_A-2xD_ctrl_B    43.34908711  19.2539183  67.4442559 0.0000005
## 2xD_salt_B-2xD_ctrl_B    21.60138633  -2.4937825  45.6965551 0.1383932
## 2xE_ctrl_A-2xD_ctrl_B    -0.44950147 -24.5446703  23.6456673 1.0000000
## 2xE_ctrl_B-2xD_ctrl_B    -4.67671726 -28.7718861  19.4184515 0.9999999
## 2xE_salt_A-2xD_ctrl_B    26.12863417   2.0334654  50.2238030 0.0193725
## 2xE_salt_B-2xD_ctrl_B    20.36944105  -3.7257277  44.4646099 0.2137797
## col_ctrl_A-2xD_ctrl_B     6.78028151 -17.3148873  30.8754503 0.9999632
## col_ctrl_B-2xD_ctrl_B    -0.32704916 -24.4222180  23.7681196 1.0000000
## col_salt_A-2xD_ctrl_B    35.51253345  11.4173646  59.6077022 0.0000911
## col_salt_B-2xD_ctrl_B    16.62216480  -7.4730040  40.7173336 0.5780741
## duf_ctrl_A-2xD_ctrl_B    -1.10625453 -25.2014233  22.9889143 1.0000000
## duf_ctrl_B-2xD_ctrl_B    -4.42045063 -28.5156194  19.6747182 1.0000000
## duf_salt_A-2xD_ctrl_B    33.58512910   9.4899603  57.6802979 0.0003042
## duf_salt_B-2xD_ctrl_B    17.47540127  -6.6197675  41.5705701 0.4829345
## wrky_ctrl_A-2xD_ctrl_B    6.73687455 -17.3582943  30.8320433 0.9999666
## wrky_ctrl_B-2xD_ctrl_B   -0.66782920 -24.7629980  23.4273396 1.0000000
## wrky_salt_A-2xD_ctrl_B   28.51405320   4.4188844  52.6092220 0.0056879
## wrky_salt_B-2xD_ctrl_B   24.61718063   0.5220118  48.7123494 0.0395655
## 2xD_salt_B-2xD_salt_A   -21.74770078 -45.8428696   2.3474680 0.1310116
## 2xE_ctrl_A-2xD_salt_A   -43.79858858 -67.8937574 -19.7034198 0.0000003
## 2xE_ctrl_B-2xD_salt_A   -48.02580438 -72.1209732 -23.9306356 0.0000000
## 2xE_salt_A-2xD_salt_A   -17.22045294 -41.3156217   6.8747159 0.5111223
## 2xE_salt_B-2xD_salt_A   -22.97964606 -47.0748149   1.1155227 0.0805408
## col_ctrl_A-2xD_salt_A   -36.56880560 -60.6639744 -12.4736368 0.0000462
## col_ctrl_B-2xD_salt_A   -43.67613627 -67.7713051 -19.5809675 0.0000004
## col_salt_A-2xD_salt_A    -7.83655367 -31.9317225  16.2586151 0.9996965
## col_salt_B-2xD_salt_A   -26.72692231 -50.8220911  -2.6317535 0.0143998
## duf_ctrl_A-2xD_salt_A   -44.45534164 -68.5505104 -20.3601728 0.0000002
## duf_ctrl_B-2xD_salt_A   -47.76953774 -71.8647065 -23.6743689 0.0000000
## duf_salt_A-2xD_salt_A    -9.76395801 -33.8591268  14.3312108 0.9947737
## duf_salt_B-2xD_salt_A   -25.87368584 -49.9688546  -1.7785170 0.0219317
## wrky_ctrl_A-2xD_salt_A  -36.61221257 -60.7073814 -12.5170438 0.0000450
## wrky_ctrl_B-2xD_salt_A  -44.01691631 -68.1120851 -19.9217475 0.0000003
## wrky_salt_A-2xD_salt_A  -14.83503391 -38.9302027   9.2601349 0.7677449
## wrky_salt_B-2xD_salt_A  -18.73190648 -42.8270753   5.3632623 0.3520437
## 2xE_ctrl_A-2xD_salt_B   -22.05088780 -46.1460566   2.0442810 0.1167050
## 2xE_ctrl_B-2xD_salt_B   -26.27810359 -50.3732724  -2.1829348 0.0180016
## 2xE_salt_A-2xD_salt_B     4.52724784 -19.5679210  28.6224166 0.9999999
## 2xE_salt_B-2xD_salt_B    -1.23194528 -25.3271141  22.8632235 1.0000000
## col_ctrl_A-2xD_salt_B   -14.82110482 -38.9162736   9.2740640 0.7690717
## col_ctrl_B-2xD_salt_B   -21.92843549 -46.0236043   2.1667333 0.1223253
## col_salt_A-2xD_salt_B    13.91114712 -10.1840217  38.0063159 0.8477827
## col_salt_B-2xD_salt_B    -4.97922153 -29.0743903  19.1159473 0.9999997
## duf_ctrl_A-2xD_salt_B   -22.70764086 -46.8028097   1.3875279 0.0900102
## duf_ctrl_B-2xD_salt_B   -26.02183696 -50.1170058  -1.9266682 0.0204096
## duf_salt_A-2xD_salt_B    11.98374278 -12.1114260  36.0789116 0.9547649
## duf_salt_B-2xD_salt_B    -4.12598506 -28.2211539  19.9691837 1.0000000
## wrky_ctrl_A-2xD_salt_B  -14.86451178 -38.9596806   9.2306570 0.7649264
## wrky_ctrl_B-2xD_salt_B  -22.26921553 -46.3643843   1.8259533 0.1071995
## wrky_salt_A-2xD_salt_B    6.91266687 -17.1825019  31.0078357 0.9999508
## wrky_salt_B-2xD_salt_B    3.01579430 -21.0793745  27.1109631 1.0000000
## 2xE_ctrl_B-2xE_ctrl_A    -4.22721579 -28.3223846  19.8679530 1.0000000
## 2xE_salt_A-2xE_ctrl_A    26.57813564   2.4829668  50.6733044 0.0155132
## 2xE_salt_B-2xE_ctrl_A    20.81894252  -3.2762263  44.9141113 0.1834483
## col_ctrl_A-2xE_ctrl_A     7.22978298 -16.8653858  31.3249518 0.9999043
## col_ctrl_B-2xE_ctrl_A     0.12245231 -23.9727165  24.2176211 1.0000000
## col_salt_A-2xE_ctrl_A    35.96203492  11.8668661  60.0572037 0.0000684
## col_salt_B-2xE_ctrl_A    17.07166627  -7.0235025  41.1668351 0.5277055
## duf_ctrl_A-2xE_ctrl_A    -0.65675306 -24.7519219  23.4384157 1.0000000
## duf_ctrl_B-2xE_ctrl_A    -3.97094916 -28.0661180  20.1242196 1.0000000
## duf_salt_A-2xE_ctrl_A    34.03463057   9.9394618  58.1297994 0.0002306
## duf_salt_B-2xE_ctrl_A    17.92490274  -6.1702661  42.0200715 0.4342888
## wrky_ctrl_A-2xE_ctrl_A    7.18637602 -16.9087928  31.2815448 0.9999124
## wrky_ctrl_B-2xE_ctrl_A   -0.21832773 -24.3134965  23.8768411 1.0000000
## wrky_salt_A-2xE_ctrl_A   28.96355467   4.8683859  53.0587235 0.0044607
## wrky_salt_B-2xE_ctrl_A   25.06668210   0.9715133  49.1618509 0.0321720
## 2xE_salt_A-2xE_ctrl_B    30.80535143   6.7101826  54.9005202 0.0015899
## 2xE_salt_B-2xE_ctrl_B    25.04615831   0.9509895  49.1413271 0.0324807
## col_ctrl_A-2xE_ctrl_B    11.45699878 -12.6381700  35.5521676 0.9704917
## col_ctrl_B-2xE_ctrl_B     4.34966811 -19.7455007  28.4448369 1.0000000
## col_salt_A-2xE_ctrl_B    40.18925071  16.0940819  64.2844195 0.0000042
## col_salt_B-2xE_ctrl_B    21.29888206  -2.7962867  45.3940509 0.1546772
## duf_ctrl_A-2xE_ctrl_B     3.57046273 -20.5247061  27.6656315 1.0000000
## duf_ctrl_B-2xE_ctrl_B     0.25626664 -23.8389022  24.3514354 1.0000000
## duf_salt_A-2xE_ctrl_B    38.26184637  14.1666776  62.3570152 0.0000152
## duf_salt_B-2xE_ctrl_B    22.15211854  -1.9430503  46.2472873 0.1122167
## wrky_ctrl_A-2xE_ctrl_B   11.41359181 -12.6815770  35.5087606 0.9715728
## wrky_ctrl_B-2xE_ctrl_B    4.00888806 -20.0862807  28.1040569 1.0000000
## wrky_salt_A-2xE_ctrl_B   33.19077047   9.0956017  57.2859393 0.0003871
## wrky_salt_B-2xE_ctrl_B   29.29389789   5.1987291  53.3890667 0.0037226
## 2xE_salt_B-2xE_salt_A    -5.75919312 -29.8543619  18.3359757 0.9999971
## col_ctrl_A-2xE_salt_A   -19.34835265 -43.4435215   4.7468161 0.2950422
## col_ctrl_B-2xE_salt_A   -26.45568333 -50.5508521  -2.3605145 0.0164881
## col_salt_A-2xE_salt_A     9.38389928 -14.7112695  33.4790681 0.9967563
## col_salt_B-2xE_salt_A    -9.50646937 -33.6016382  14.5886994 0.9962017
## duf_ctrl_A-2xE_salt_A   -27.23488870 -51.3300575  -3.1397199 0.0111288
## duf_ctrl_B-2xE_salt_A   -30.54908479 -54.6442536  -6.4539160 0.0018414
## duf_salt_A-2xE_salt_A     7.45649494 -16.6386739  31.5516637 0.9998502
## duf_salt_B-2xE_salt_A    -8.65323289 -32.7484017  15.4419359 0.9988378
## wrky_ctrl_A-2xE_salt_A  -19.39175962 -43.4869284   4.7034092 0.2912446
## wrky_ctrl_B-2xE_salt_A  -26.79646337 -50.8916322  -2.7012946 0.0139050
## wrky_salt_A-2xE_salt_A    2.38541904 -21.7097498  26.4805878 1.0000000
## wrky_salt_B-2xE_salt_A   -1.51145354 -25.6066223  22.5837153 1.0000000
## col_ctrl_A-2xE_salt_B   -13.58915954 -37.6843283  10.5060093 0.8714705
## col_ctrl_B-2xE_salt_B   -20.69649021 -44.7916590   3.3986786 0.1913824
## col_salt_A-2xE_salt_B    15.14309239  -8.9520764  39.2382612 0.7375969
## col_salt_B-2xE_salt_B    -3.74727625 -27.8424450  20.3478925 1.0000000
## duf_ctrl_A-2xE_salt_B   -21.47569558 -45.5708644   2.6194732 0.1449898
## duf_ctrl_B-2xE_salt_B   -24.78989168 -48.8850605  -0.6947229 0.0365634
## duf_salt_A-2xE_salt_B    13.21568805 -10.8794807  37.3108569 0.8960050
## duf_salt_B-2xE_salt_B    -2.89403978 -26.9892086  21.2011290 1.0000000
## wrky_ctrl_A-2xE_salt_B  -13.63256651 -37.7277353  10.4626023 0.8684126
## wrky_ctrl_B-2xE_salt_B  -21.03727025 -45.1324390   3.0578985 0.1699049
## wrky_salt_A-2xE_salt_B    8.14461215 -15.9505566  32.2397810 0.9994828
## wrky_salt_B-2xE_salt_B    4.24773958 -19.8474292  28.3429084 1.0000000
## col_ctrl_B-col_ctrl_A    -7.10733067 -31.2024995  16.9878381 0.9999256
## col_salt_A-col_ctrl_A    28.73225193   4.6370831  52.8274207 0.0050572
## col_salt_B-col_ctrl_A     9.84188329 -14.2532855  33.9370521 0.9942622
## duf_ctrl_A-col_ctrl_A    -7.88653604 -31.9817048  16.2086328 0.9996683
## duf_ctrl_B-col_ctrl_A   -11.20073214 -35.2959009  12.8944367 0.9764431
## duf_salt_A-col_ctrl_A    26.80484759   2.7096788  50.9000164 0.0138464
## duf_salt_B-col_ctrl_A    10.69511976 -13.4000490  34.7902886 0.9854323
## wrky_ctrl_A-col_ctrl_A   -0.04340697 -24.1385758  24.0517618 1.0000000
## wrky_ctrl_B-col_ctrl_A   -7.44811071 -31.5432795  16.6470581 0.9998526
## wrky_salt_A-col_ctrl_A   21.73377169  -2.3613971  45.8289405 0.1317007
## wrky_salt_B-col_ctrl_A   17.83689912  -6.2582697  41.9320679 0.4436829
## col_salt_A-col_ctrl_B    35.83958260  11.7444138  59.9347514 0.0000740
## col_salt_B-col_ctrl_B    16.94921396  -7.1459548  41.0443828 0.5414026
## duf_ctrl_A-col_ctrl_B    -0.77920537 -24.8743742  23.3159634 1.0000000
## duf_ctrl_B-col_ctrl_B    -4.09340147 -28.1885703  20.0017673 1.0000000
## duf_salt_A-col_ctrl_B    33.91217826   9.8170095  58.0073471 0.0002487
## duf_salt_B-col_ctrl_B    17.80245043  -6.2927184  41.8976192 0.4473790
## wrky_ctrl_A-col_ctrl_B    7.06392370 -17.0312451  31.1590925 0.9999320
## wrky_ctrl_B-col_ctrl_B   -0.34078004 -24.4359488  23.7543888 1.0000000
## wrky_salt_A-col_ctrl_B   28.84110236   4.7459336  52.9362712 0.0047677
## wrky_salt_B-col_ctrl_B   24.94422979   0.8490610  49.0393986 0.0340533
## col_salt_B-col_salt_A   -18.89036864 -42.9855374   5.2048002 0.3368614
## duf_ctrl_A-col_salt_A   -36.61878798 -60.7139568 -12.5236192 0.0000448
## duf_ctrl_B-col_salt_A   -39.93298407 -64.0281529 -15.8378153 0.0000050
## duf_salt_A-col_salt_A    -1.92740434 -26.0225731  22.1677645 1.0000000
## duf_salt_B-col_salt_A   -18.03713217 -42.1323010   6.0580366 0.4224147
## wrky_ctrl_A-col_salt_A  -28.77565890 -52.8708277  -4.6804901 0.0049398
## wrky_ctrl_B-col_salt_A  -36.18036264 -60.2755314 -12.0851938 0.0000594
## wrky_salt_A-col_salt_A   -6.99848024 -31.0936490  17.0966886 0.9999408
## wrky_salt_B-col_salt_A  -10.89535282 -34.9905216  13.1998160 0.9822731
## duf_ctrl_A-col_salt_B   -17.72841933 -41.8235881   6.3667495 0.4553560
## duf_ctrl_B-col_salt_B   -21.04261543 -45.1377842   3.0525534 0.1695829
## duf_salt_A-col_salt_B    16.96296430  -7.1322045  41.0581331 0.5398629
## duf_salt_B-col_salt_B     0.85323647 -23.2419323  24.9484053 1.0000000
## wrky_ctrl_A-col_salt_B   -9.88529026 -33.9804591  14.2098785 0.9939597
## wrky_ctrl_B-col_salt_B  -17.28999400 -41.3851628   6.8051748 0.5034013
## wrky_salt_A-col_salt_B   11.89188840 -12.2032804  35.9870572 0.9578725
## wrky_salt_B-col_salt_B    7.99501583 -16.1001530  32.0901846 0.9995991
## duf_ctrl_B-duf_ctrl_A    -3.31419610 -27.4093649  20.7809727 1.0000000
## duf_salt_A-duf_ctrl_A    34.69138363  10.5962148  58.7865524 0.0001531
## duf_salt_B-duf_ctrl_A    18.58165580  -5.5135130  42.6768246 0.3667563
## wrky_ctrl_A-duf_ctrl_A    7.84312907 -16.2520397  31.9382979 0.9996929
## wrky_ctrl_B-duf_ctrl_A    0.43842533 -23.6567435  24.5335941 1.0000000
## wrky_salt_A-duf_ctrl_A   29.62030773   5.5251389  53.7154765 0.0031077
## wrky_salt_B-duf_ctrl_A   25.72343516   1.6282664  49.8186040 0.0235797
## duf_salt_A-duf_ctrl_B    38.00557973  13.9104109  62.1007485 0.0000180
## duf_salt_B-duf_ctrl_B    21.89585190  -2.1993169  45.9910207 0.1238566
## wrky_ctrl_A-duf_ctrl_B   11.15732517 -12.9378436  35.2524940 0.9773519
## wrky_ctrl_B-duf_ctrl_B    3.75262143 -20.3425474  27.8477902 1.0000000
## wrky_salt_A-duf_ctrl_B   32.93450383   8.8393350  57.0296726 0.0004523
## wrky_salt_B-duf_ctrl_B   29.03763126   4.9424625  53.1328001 0.0042841
## duf_salt_B-duf_salt_A   -16.10972783 -40.2048966   7.9854410 0.6351626
## wrky_ctrl_A-duf_salt_A  -26.84825456 -50.9434234  -2.7530858 0.0135467
## wrky_ctrl_B-duf_salt_A  -34.25295830 -58.3481271 -10.1577895 0.0002014
## wrky_salt_A-duf_salt_A   -5.07107590 -29.1662447  19.0240929 0.9999996
## wrky_salt_B-duf_salt_A   -8.96794847 -33.0631173  15.1272203 0.9981577
## wrky_ctrl_A-duf_salt_B  -10.73852673 -34.8336955  13.3566421 0.9847888
## wrky_ctrl_B-duf_salt_B  -18.14323047 -42.2383993   5.9519383 0.4113060
## wrky_salt_A-duf_salt_B   11.03865193 -13.0565169  35.1338207 0.9796980
## wrky_salt_B-duf_salt_B    7.14177936 -16.9533894  31.2369482 0.9999201
## wrky_ctrl_B-wrky_ctrl_A  -7.40470374 -31.4998725  16.6904651 0.9998645
## wrky_salt_A-wrky_ctrl_A  21.77717866  -2.3179901  45.8723475 0.1295625
## wrky_salt_B-wrky_ctrl_A  17.88030608  -6.2148627  41.9754749 0.4390406
## wrky_salt_A-wrky_ctrl_B  29.18188240   5.0867136  53.2770512 0.0039589
## wrky_salt_B-wrky_ctrl_B  25.28500983   1.1898410  49.3801786 0.0290466
## wrky_salt_B-wrky_salt_A  -3.89687257 -27.9920414  20.1982962 1.0000000
P7 = Output$All.ID[,'p adj']
stat.test<- multcompLetters(P7)
stat.test
##  2xD_ctrl_B  2xD_salt_A  2xD_salt_B  2xE_ctrl_A  2xE_ctrl_B  2xE_salt_A 
##        "ab"         "c"     "acdef"        "ab"         "b"       "cde" 
##  2xE_salt_B  col_ctrl_A  col_ctrl_B  col_salt_A  col_salt_B  duf_ctrl_A 
##     "acdef"      "abdf"        "ab"        "ce"     "abdef"        "ab" 
##  duf_ctrl_B  duf_salt_A  duf_salt_B wrky_ctrl_A wrky_ctrl_B wrky_salt_A 
##         "b"        "ce"     "abdef"      "abdf"        "ab"       "cde" 
## wrky_salt_B  2xD_ctrl_A 
##      "cdef"       "abf"
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
test
###################################################################
test$info <- strsplit(test$group1, "_")
test$info[[1]][2]
## [1] "ctrl"
test$Geno <- "none"
test$Condition<- "none"
test$Tray<- "none"
test
for(i in 1:nrow(test)){
  test$Geno[i] <- test$info[[i]][1]
  test$Condition[i] <- test$info[[i]][2]
  test$Tray[i] <- test$info[[i]][3]  
}
#whatever x-axis is going to be, my test group should be the same. 
test2 <- test[,c(5:7,1)]
test2$group1 <- test2$Geno
test2$group2 <- test2$Geno
test2
IL$Geno<- factor(IL$Geno, levels=c("col", "duf", "wrky","2xD", "2xE"))

IL_graph <- ggplot(data = IL, mapping = aes(x = Geno, y = Ion.leakage, colour = Geno)) 
IL_graph <- IL_graph + geom_boxplot(alpha=0.2) + geom_jitter(width=0.1,alpha=0.2)

IL_graph <- IL_graph + facet_grid(Tray ~ Condition, scales = "free_y")

IL_graph <- IL_graph + stat_summary(fun=mean, geom="point", shape=95, size=6, color="black", fill="black")
IL_graph <- IL_graph + scale_color_manual(values = c("blue","blueviolet","cyan", "red", "deeppink", "magenta"))
IL_graph <- IL_graph + ylab("Shoot ion leakage, %") + xlab("") + stat_pvalue_manual(test2, label = "Tukey", y.position = 80)
IL_graph <- IL_graph + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
IL_graph <- IL_graph + rremove("legend")
IL_graph