R Notebook

list.files(pattern = "csv")

##  [1] "20240402_CSHL-15-TEST.csv"                   
##  [2] "aero_drought_sim_20240621.csv"               
##  [3] "cowpea_combining_csv"                        
##  [4] "Exp_90_Arabidopsis_DUF247_BEFORE_curated.csv"
##  [5] "Exp_91_Arabidopsis_DUF247_AFTER_curated.csv" 
##  [6] "ICPMS_average_HS_20240529.csv"               
##  [7] "ICPMS_curated_HS_20240530.csv"               
##  [8] "multifacet_test.csv"                         
##  [9] "PhotosynQ_aeroponics_HS_20240313.csv"        
## [10] "RSA_RNAi_1.csv"                              
## [11] "RSA_RNAi_2.csv"                              
## [12] "RSA_RNAi_3_4.csv"                            
## [13] "RSA_RNAi_dufOE_updated.csv"                  
## [14] "RSA2_improved_tracing.csv"                   
## [15] "RSA3_root_tracing_HS.csv"                    
## [16] "RSA4_20231016_24_HS.csv"                     
## [17] "Tray_key_match.csv"

dataB <- read.csv("Exp_90_Arabidopsis_DUF247_BEFORE_curated.csv")
dataA <- read.csv("Exp_91_Arabidopsis_DUF247_AFTER_curated.csv")
key <- read.csv("Tray_key_match.csv")

dataA

dataB

key

colnames(key)[2] <- "Cell"
library(reshape2)

## Warning: package 'reshape2' was built under R version 4.3.2

dataAk <- merge(key, dataA, by = c("Tray_match", "Cell"), all = T)
dataBk <- merge(key, dataB, by = c("Tray_match", "Cell"), all = T)
dataAk

dataBk

colnames(dataAk)

##  [1] "Tray_match" "Cell"       "treatment"  "mutant"     "BTI.name"  
##  [6] "File"       "Exp."       "Tray"       "Round"      "TOD"       
## [11] "DOE"        "Date"       "Time"       "Roi.No"     "Roi.Mask"  
## [16] "Roi.Xc"     "Roi.Yc"     "Fv.Fm"      "Fq..Fm."    "rETR"      
## [21] "SpcGrn"     "FarRed"     "Nir"        "ChlIdx"     "AriIdx"    
## [26] "NDVI"

colnames(dataBk)

##  [1] "Tray_match" "Cell"       "treatment"  "mutant"     "BTI.name"  
##  [6] "File"       "DOE"        "Date"       "Time"       "TOD"       
## [11] "Roi.No"     "Roi.Mask"   "Roi.Xc"     "Roi.Yc"     "Fv.Fm"     
## [16] "Fq..Fm."    "rETR"       "Red"        "Green"      "Blue"      
## [21] "Hue"        "Saturation" "Value"      "SpcGrn"     "FarRed"    
## [26] "Nir"        "ChlIdx"     "AriIdx"     "NDVI"       "Exp"       
## [31] "Tray"       "Round"

dataAk <- dataAk[,c(1:6, 10:26)]
dataBk <- dataBk[,c(1:6, 10, 7:9, 11:17, 24:29)]

colnames(dataAk) %in% colnames(dataBk)

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

colnames(dataAk)

##  [1] "Tray_match" "Cell"       "treatment"  "mutant"     "BTI.name"  
##  [6] "File"       "TOD"        "DOE"        "Date"       "Time"      
## [11] "Roi.No"     "Roi.Mask"   "Roi.Xc"     "Roi.Yc"     "Fv.Fm"     
## [16] "Fq..Fm."    "rETR"       "SpcGrn"     "FarRed"     "Nir"       
## [21] "ChlIdx"     "AriIdx"     "NDVI"

colnames(dataBk)

##  [1] "Tray_match" "Cell"       "treatment"  "mutant"     "BTI.name"  
##  [6] "File"       "TOD"        "DOE"        "Date"       "Time"      
## [11] "Roi.No"     "Roi.Mask"   "Roi.Xc"     "Roi.Yc"     "Fv.Fm"     
## [16] "Fq..Fm."    "rETR"       "SpcGrn"     "FarRed"     "Nir"       
## [21] "ChlIdx"     "AriIdx"     "NDVI"

data <- rbind(dataAk, dataBk)
data

decode date and time into a more reliable time unit

unique(data$Date)

##  [1] 20240210 20240208 20240206 20240216 20240205 20240218 20240203 20240217
##  [9] 20240211 20240219 20240207 20240212 20240202 20240209 20240220 20240204
## [17] 20240213 20240201 20240131       NA 20240130 20240129 20240128 20240127
## [25] 20240125 20240126

unique(data$Time)

##   [1] "2:06"  "14:06" "21:41" "2:08"  "7:57"  "14:08" "5:43"  "0:35"  "19:19"
##  [10] "5:35"  "13:56" "6:12"  "16:19" "2:49"  "17:53" "4:22"  "2:09"  "17:54"
##  [19] "5:44"  "6:14"  "5:36"  "2:51"  "16:20" "13:58" "2:07"  "0:37"  "14:10"
##  [28] "4:24"  "7:59"  "19:21" "21:43" NA      "14:00" "14:12" "2:11"  "19:23"
##  [37] "0:38"  "8:01"  "2:53"  "16:22" "5:46"  "14:09" "17:56" "5:38"  "4:26" 
##  [46] "6:15"  "2:13"  "6:20"  "5:42"  "8:06"  "14:15" "14:17" "2:16"  "14:14"
##  [55] "21:50" "4:31"  "0:44"  "16:27" "18:00" "2:58"  "5:52"  "19:29" "14:11"
##  [64] "0:40"  "6:17"  "2:10"  "8:02"  "16:24" "2:54"  "19:25" "5:48"  "21:46"
##  [73] "14:02" "4:27"  "17:57" "21:52" "2:18"  "14:19" "2:17"  "16:29" "14:16"
##  [82] "8:07"  "19:31" "2:14"  "2:15"  "6:21"  "5:54"  "4:33"  "2:59"  "0:46" 
##  [91] "18:01" "2:19"  "14:18" "6:23"  "21:53" "4:34"  "16:31" "14:21" "0:48" 
## [100] "5:56"  "8:09"  "18:03" "5:45"  "19:33" "14:23" "0:50"  "5:58"  "2:21" 
## [109] "14:20" "8:11"  "6:24"  "5:47"  "4:36"  "3:02"  "19:35" "16:32" "2:20" 
## [118] "21:55" "18:04" "2:12"  "21:48" "0:42"  "5:50"  "14:13" "8:04"  "17:58"
## [127] "6:18"  "14:04" "16:25" "5:41"  "2:56"  "4:29"  "19:27" "6:02"  "2:23" 
## [136] "2:24"  "18:07" "4:39"  "0:54"  "14:27" "8:14"  "19:38" "5:49"  "6:27" 
## [145] "16:36" "3:06"  "21:58" "14:28" "6:31"  "14:33" "2:28"  "16:41" "19:44"
## [154] "22:03" "0:59"  "3:11"  "6:07"  "2:29"  "2:25"  "18:11" "4:44"  "8:19" 
## [163] "5:53"  "14:25" "2:22"  "18:09" "6:28"  "14:29" "16:38" "19:40" "22:00"
## [172] "0:55"  "3:07"  "6:03"  "8:16"  "2:26"  "4:41"  "5:51"  "3:04"  "14:22"
## [181] "6:26"  "8:12"  "21:57" "16:34" "0:52"  "6:00"  "19:37" "18:06" "4:38" 
## [190] "22:01" "14:26" "18:10" "14:31" "2:27"  "8:17"  "16:39" "3:09"  "6:05" 
## [199] "4:43"  "0:57"  "6:30"  "19:42" "5:11"  "15:23" "5:16"  "15:29" "5:22" 
## [208] "5:27"  "15:35" "2:32"  "5:33"  "2:37"  "2:43"  "15:47" "15:52" "2:48" 
## [217] "5:55"  "6:06"  "3:05"  "14:24" "3:10"  "6:11"  "3:16"  "3:21"

data_day <- subset(dataAk, data$TOD == "Light")
data_night <- subset(dataAk, data$TOD == "Dark")
data_day

data_day$POT <- paste(data_day$Tray_match, "_", data_day$Cell)
data_night$POT <- paste(data_night$Tray_match, "_", data_night$Cell)
bye <- c(20, 21)

data_day2 <- subset(data_day, !(data_day$DOE %in% bye))
data_day2 <- na.omit(data_day2)
library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.3.2

library(ggpubr)

## Warning: package 'ggpubr' was built under R version 4.3.2

Roimask_CvS <- ggplot(data = data_day2, aes(x = DOE, y = Roi.Mask, color = treatment, group = POT)) + theme_classic()
Roimask_CvS <- Roimask_CvS + geom_line(alpha = 0.1)
Roimask_CvS <- Roimask_CvS + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = treatment), alpha = 0.3) + stat_summary(fun = mean, aes(group = treatment), size = 0.9, geom = "line", linetype = "solid")

## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

Roimask_CvS <- Roimask_CvS + stat_compare_means(aes(group = treatment), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_CvS <- Roimask_CvS + scale_color_manual(values = c("blue", "red"))
Roimask_CvS <- Roimask_CvS + xlab("Days After Stress") + ylab("Average Leaf Area") + ggtitle("Control v Salt - Roi.mask over time") + theme(legend.position="bottom")
Roimask_CvS

#look for outliers/lines with only one plant
lines1 <- c("m1", "col-0")
m1_v_C <- subset(data_day, data_day$mutant %in% lines1)
m1_v_C

Roimask_m1vC <- ggplot(data = m1_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m1vC <- Roimask_m1vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m1vC <- Roimask_m1vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m1vC <- Roimask_m1vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m1vC <- Roimask_m1vC + scale_color_manual(values = c("blue", "red"))
Roimask_m1vC <- Roimask_m1vC + xlab("Days After Stress") + ggtitle("CSHL4 D1c3 vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m1vC

Fq..Fm._m1vC <- ggplot(data = m1_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m1vC <- Fq..Fm._m1vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m1vC <- Fq..Fm._m1vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m1vC <- Fq..Fm._m1vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m1vC <- Fq..Fm._m1vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m1vC <- Fq..Fm._m1vC + xlab("Days After Stress") + ggtitle("CSHL4 D1c3 vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m1vC

ChlIdx_m1vC <- ggplot(data = m1_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m1vC <- ChlIdx_m1vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m1vC <- ChlIdx_m1vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m1vC <- ChlIdx_m1vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m1vC <- ChlIdx_m1vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m1vC <- ChlIdx_m1vC + xlab("Days After Stress") + ggtitle("CSHL4 D1c3 vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m1vC

AriIdx_m1vC <- ggplot(data = m1_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m1vC <- AriIdx_m1vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m1vC <- AriIdx_m1vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m1vC <- AriIdx_m1vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m1vC <- AriIdx_m1vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m1vC <- AriIdx_m1vC + xlab("Days After Stress") + ggtitle("CSHL4 D1c3 vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m1vC

NDVI_m1vC <- ggplot(data = m1_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m1vC <- NDVI_m1vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m1vC <- NDVI_m1vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m1vC <- NDVI_m1vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m1vC <- NDVI_m1vC + scale_color_manual(values = c("blue", "red"))
NDVI_m1vC <- NDVI_m1vC + xlab("Days After Stress") + ggtitle("CSHL4 D1c3 vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m1vC

lines2 <- c("m2", "col-0")
m2_v_C <- subset(data_day, data_day$mutant %in% lines2)

lines3 <- c("m3", "col-0")
m3_v_C <- subset(data_day, data_day$mutant %in% lines3)

lines4 <- c("m4", "col-0")
m4_v_C <- subset(data_day, data_day$mutant %in% lines4)

lines5 <- c("m5", "col-0")
m5_v_C <- subset(data_day, data_day$mutant %in% lines5)

lines6 <- c("m6", "col-0")
m6_v_C <- subset(data_day, data_day$mutant %in% lines6)

lines7 <- c("m7", "col-0")
m7_v_C <- subset(data_day, data_day$mutant %in% lines7)

lines8 <- c("m8", "col-0")
m8_v_C <- subset(data_day, data_day$mutant %in% lines8)

lines9 <- c("m9", "col-0")
m9_v_C <- subset(data_day, data_day$mutant %in% lines9)

lines10 <- c("m10", "col-0")
m10_v_C <- subset(data_day, data_day$mutant %in% lines10)

lines11 <- c("m11", "col-0")
m11_v_C <- subset(data_day, data_day$mutant %in% lines11)

lines12 <- c("m12", "col-0")
m12_v_C <- subset(data_day, data_day$mutant %in% lines12)

lines13 <- c("m13", "col-0")
m13_v_C <- subset(data_day, data_day$mutant %in% lines13)

lines14 <- c("m14", "col-0")
m14_v_C <- subset(data_day, data_day$mutant %in% lines14)

lines15 <- c("m15", "col-0")
m15_v_C <- subset(data_day, data_day$mutant %in% lines15)

Roimask_m2vC <- ggplot(data = m2_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m2vC <- Roimask_m2vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m2vC <- Roimask_m2vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m2vC <- Roimask_m2vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m2vC <- Roimask_m2vC + scale_color_manual(values = c("blue", "red"))
Roimask_m2vC <- Roimask_m2vC + xlab("Days After Stress") + ggtitle("CSHL8 G2b vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m2vC

Fq..Fm._m2vC <- ggplot(data = m2_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m2vC <- Fq..Fm._m2vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m2vC <- Fq..Fm._m2vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m2vC <- Fq..Fm._m2vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m2vC <- Fq..Fm._m2vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m2vC <- Fq..Fm._m2vC + xlab("Days After Stress") + ggtitle("CSHL8 G2b vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m2vC

ChlIdx_m2vC <- ggplot(data = m2_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m2vC <- ChlIdx_m2vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m2vC <- ChlIdx_m2vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m2vC <- ChlIdx_m2vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m2vC <- ChlIdx_m2vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m2vC <- ChlIdx_m2vC + xlab("Days After Stress") + ggtitle("CSHL8 G2b vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m2vC

AriIdx_m2vC <- ggplot(data = m2_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m2vC <- AriIdx_m2vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m2vC <- AriIdx_m2vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m2vC <- AriIdx_m2vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m2vC <- AriIdx_m2vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m2vC <- AriIdx_m2vC + xlab("Days After Stress") + ggtitle("CSHL8 G2b vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m2vC

NDVI_m2vC <- ggplot(data = m2_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m2vC <- NDVI_m2vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m2vC <- NDVI_m2vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m2vC <- NDVI_m2vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m2vC <- NDVI_m2vC + scale_color_manual(values = c("blue", "red"))
NDVI_m2vC <- NDVI_m2vC + xlab("Days After Stress") + ggtitle("CSHL8 G2b vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m2vC

Roimask_m3vC <- ggplot(data = m3_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m3vC <- Roimask_m3vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m3vC <- Roimask_m3vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m3vC <- Roimask_m3vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m3vC <- Roimask_m3vC + scale_color_manual(values = c("blue", "red"))
Roimask_m3vC <- Roimask_m3vC + xlab("Days After Stress") + ggtitle("CSHL10 I1c vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m3vC

Fq..Fm._m3vC <- ggplot(data = m3_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m3vC <- Fq..Fm._m3vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m3vC <- Fq..Fm._m3vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m3vC <- Fq..Fm._m3vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m3vC <- Fq..Fm._m3vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m3vC <- Fq..Fm._m3vC + xlab("Days After Stress") + ggtitle("CSHL10 I1c vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m3vC

ChlIdx_m3vC <- ggplot(data = m3_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m3vC <- ChlIdx_m3vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m3vC <- ChlIdx_m3vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m3vC <- ChlIdx_m3vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m3vC <- ChlIdx_m3vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m3vC <- ChlIdx_m3vC + xlab("Days After Stress") + ggtitle("CSHL10 I1c vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m3vC

AriIdx_m3vC <- ggplot(data = m3_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m3vC <- AriIdx_m3vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m3vC <- AriIdx_m3vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m3vC <- AriIdx_m3vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m3vC <- AriIdx_m3vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m3vC <- AriIdx_m3vC + xlab("Days After Stress") + ggtitle("CSHL10 I1c vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m3vC

NDVI_m3vC <- ggplot(data = m3_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m3vC <- NDVI_m3vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m3vC <- NDVI_m3vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m3vC <- NDVI_m3vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m3vC <- NDVI_m3vC + scale_color_manual(values = c("blue", "red"))
NDVI_m3vC <- NDVI_m3vC + xlab("Days After Stress") + ggtitle("CSHL10 I1c vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m3vC

Roimask_m4vC <- ggplot(data = m4_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m4vC <- Roimask_m4vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m4vC <- Roimask_m4vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m4vC <- Roimask_m4vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m4vC <- Roimask_m4vC + scale_color_manual(values = c("blue", "red"))
Roimask_m4vC <- Roimask_m4vC + xlab("Days After Stress") + ggtitle("CSHL12 A1a vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m4vC

Fq..Fm._m4vC <- ggplot(data = m4_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m4vC <- Fq..Fm._m4vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m4vC <- Fq..Fm._m4vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m4vC <- Fq..Fm._m4vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m4vC <- Fq..Fm._m4vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m4vC <- Fq..Fm._m4vC + xlab("Days After Stress") + ggtitle("CSHL12 A1a vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m4vC

ChlIdx_m4vC <- ggplot(data = m4_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m4vC <- ChlIdx_m4vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m4vC <- ChlIdx_m4vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m4vC <- ChlIdx_m4vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m4vC <- ChlIdx_m4vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m4vC <- ChlIdx_m4vC + xlab("Days After Stress") + ggtitle("CSHL12 A1a vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m4vC

AriIdx_m4vC <- ggplot(data = m4_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m4vC <- AriIdx_m4vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m4vC <- AriIdx_m4vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m4vC <- AriIdx_m4vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m4vC <- AriIdx_m4vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m4vC <- AriIdx_m4vC + xlab("Days After Stress") + ggtitle("CSHL12 A1a vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m4vC

NDVI_m4vC <- ggplot(data = m4_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m4vC <- NDVI_m4vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m4vC <- NDVI_m4vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m4vC <- NDVI_m4vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m4vC <- NDVI_m4vC + scale_color_manual(values = c("blue", "red"))
NDVI_m4vC <- NDVI_m4vC + xlab("Days After Stress") + ggtitle("CSHL12 A1a vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m4vC

Roimask_m5vC <- ggplot(data = m5_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m5vC <- Roimask_m5vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m5vC <- Roimask_m5vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m5vC <- Roimask_m5vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m5vC <- Roimask_m5vC + scale_color_manual(values = c("blue", "red"))
Roimask_m5vC <- Roimask_m5vC + xlab("Days After Stress") + ggtitle("CSHL15 E1b vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m5vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 1.
## ℹ With name: x.14.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

Fq..Fm._m5vC <- ggplot(data = m5_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m5vC <- Fq..Fm._m5vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m5vC <- Fq..Fm._m5vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m5vC <- Fq..Fm._m5vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m5vC <- Fq..Fm._m5vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m5vC <- Fq..Fm._m5vC + xlab("Days After Stress") + ggtitle("CSHL15 E1b vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m5vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 1.
## ℹ With name: x.14.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

ChlIdx_m5vC <- ggplot(data = m5_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m5vC <- ChlIdx_m5vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m5vC <- ChlIdx_m5vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m5vC <- ChlIdx_m5vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m5vC <- ChlIdx_m5vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m5vC <- ChlIdx_m5vC + xlab("Days After Stress") + ggtitle("CSHL15 E1b vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m5vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 1.
## ℹ With name: x.14.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

AriIdx_m5vC <- ggplot(data = m5_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m5vC <- AriIdx_m5vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m5vC <- AriIdx_m5vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m5vC <- AriIdx_m5vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m5vC <- AriIdx_m5vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m5vC <- AriIdx_m5vC + xlab("Days After Stress") + ggtitle("CSHL15 E1b vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m5vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 1.
## ℹ With name: x.14.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

NDVI_m5vC <- ggplot(data = m5_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m5vC <- NDVI_m5vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m5vC <- NDVI_m5vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m5vC <- NDVI_m5vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m5vC <- NDVI_m5vC + scale_color_manual(values = c("blue", "red"))
NDVI_m5vC <- NDVI_m5vC + xlab("Days After Stress") + ggtitle("CSHL15 E1b vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m5vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 1.
## ℹ With name: x.14.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

Roimask_m6vC <- ggplot(data = m6_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m6vC <- Roimask_m6vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m6vC <- Roimask_m6vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m6vC <- Roimask_m6vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m6vC <- Roimask_m6vC + scale_color_manual(values = c("blue", "red"))
Roimask_m6vC <- Roimask_m6vC + xlab("Days After Stress") + ggtitle("CSHL16 A2c vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m6vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 7.
## ℹ With name: x.9.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

Fq..Fm._m6vC <- ggplot(data = m6_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m6vC <- Fq..Fm._m6vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m6vC <- Fq..Fm._m6vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m6vC <- Fq..Fm._m6vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m6vC <- Fq..Fm._m6vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m6vC <- Fq..Fm._m6vC + xlab("Days After Stress") + ggtitle("CSHL16 A2c vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m6vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 7.
## ℹ With name: x.9.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

ChlIdx_m6vC <- ggplot(data = m6_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m6vC <- ChlIdx_m6vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m6vC <- ChlIdx_m6vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m6vC <- ChlIdx_m6vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m6vC <- ChlIdx_m6vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m6vC <- ChlIdx_m6vC + xlab("Days After Stress") + ggtitle("CSHL16 A2c vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m6vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 7.
## ℹ With name: x.9.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

AriIdx_m6vC <- ggplot(data = m6_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m6vC <- AriIdx_m6vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m6vC <- AriIdx_m6vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m6vC <- AriIdx_m6vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m6vC <- AriIdx_m6vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m6vC <- AriIdx_m6vC + xlab("Days After Stress") + ggtitle("CSHL16 A2c vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m6vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 7.
## ℹ With name: x.9.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

NDVI_m6vC <- ggplot(data = m6_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m6vC <- NDVI_m6vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m6vC <- NDVI_m6vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m6vC <- NDVI_m6vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m6vC <- NDVI_m6vC + scale_color_manual(values = c("blue", "red"))
NDVI_m6vC <- NDVI_m6vC + xlab("Days After Stress") + ggtitle("CSHL16 A2c vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m6vC

## Warning: Computation failed in `stat_compare_means()`
## Caused by error in `mutate()`:
## ℹ In argument: `p = purrr::map(...)`.
## Caused by error in `purrr::map()`:
## ℹ In index: 7.
## ℹ With name: x.9.
## Caused by error in `t.test.default()`:
## ! not enough 'y' observations

Roimask_m7vC <- ggplot(data = m7_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m7vC <- Roimask_m7vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m7vC <- Roimask_m7vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m7vC <- Roimask_m7vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m7vC <- Roimask_m7vC + scale_color_manual(values = c("blue", "red"))
Roimask_m7vC <- Roimask_m7vC + xlab("Days After Stress") + ggtitle("CSHL18 E4c vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m7vC

Fq..Fm._m7vC <- ggplot(data = m7_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m7vC <- Fq..Fm._m7vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m7vC <- Fq..Fm._m7vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m7vC <- Fq..Fm._m7vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m7vC <- Fq..Fm._m7vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m7vC <- Fq..Fm._m7vC + xlab("Days After Stress") + ggtitle("CSHL18 E4c vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m7vC

ChlIdx_m7vC <- ggplot(data = m7_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m7vC <- ChlIdx_m7vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m7vC <- ChlIdx_m7vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m7vC <- ChlIdx_m7vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m7vC <- ChlIdx_m7vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m7vC <- ChlIdx_m7vC + xlab("Days After Stress") + ggtitle("CSHL18 E4c vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m7vC

AriIdx_m7vC <- ggplot(data = m7_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m7vC <- AriIdx_m7vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m7vC <- AriIdx_m7vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m7vC <- AriIdx_m7vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m7vC <- AriIdx_m7vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m7vC <- AriIdx_m7vC + xlab("Days After Stress") + ggtitle("CSHL18 E4c vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m7vC

NDVI_m7vC <- ggplot(data = m7_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m7vC <- NDVI_m7vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m7vC <- NDVI_m7vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m7vC <- NDVI_m7vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m7vC <- NDVI_m7vC + scale_color_manual(values = c("blue", "red"))
NDVI_m7vC <- NDVI_m7vC + xlab("Days After Stress") + ggtitle("CSHL18 E4c vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m7vC

Roimask_m8vC <- ggplot(data = m8_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m8vC <- Roimask_m8vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m8vC <- Roimask_m8vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m8vC <- Roimask_m8vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m8vC <- Roimask_m8vC + scale_color_manual(values = c("blue", "red"))
Roimask_m8vC <- Roimask_m8vC + xlab("Days After Stress") + ggtitle("CSHL19 I3c vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m8vC

Fq..Fm._m8vC <- ggplot(data = m8_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m8vC <- Fq..Fm._m8vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m8vC <- Fq..Fm._m8vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m8vC <- Fq..Fm._m8vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m8vC <- Fq..Fm._m8vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m8vC <- Fq..Fm._m8vC + xlab("Days After Stress") + ggtitle("CSHL19 I3c vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m8vC

ChlIdx_m8vC <- ggplot(data = m8_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m8vC <- ChlIdx_m8vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m8vC <- ChlIdx_m8vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m8vC <- ChlIdx_m8vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m8vC <- ChlIdx_m8vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m8vC <- ChlIdx_m8vC + xlab("Days After Stress") + ggtitle("CSHL19 I3c vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m8vC

AriIdx_m8vC <- ggplot(data = m8_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m8vC <- AriIdx_m8vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m8vC <- AriIdx_m8vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m8vC <- AriIdx_m8vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m8vC <- AriIdx_m8vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m8vC <- AriIdx_m8vC + xlab("Days After Stress") + ggtitle("CSHL19 I3c vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m8vC

NDVI_m8vC <- ggplot(data = m8_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m8vC <- NDVI_m8vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m8vC <- NDVI_m8vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m8vC <- NDVI_m8vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m8vC <- NDVI_m8vC + scale_color_manual(values = c("blue", "red"))
NDVI_m8vC <- NDVI_m8vC + xlab("Days After Stress") + ggtitle("CSHL19 I3c vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m8vC

Roimask_m9vC <- ggplot(data = m9_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m9vC <- Roimask_m9vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m9vC <- Roimask_m9vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m9vC <- Roimask_m9vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m9vC <- Roimask_m9vC + scale_color_manual(values = c("blue", "red"))
Roimask_m9vC <- Roimask_m9vC + xlab("Days After Stress") + ggtitle("CSHL20 F2b vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m9vC

Fq..Fm._m9vC <- ggplot(data = m9_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m9vC <- Fq..Fm._m9vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m9vC <- Fq..Fm._m9vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m9vC <- Fq..Fm._m9vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m9vC <- Fq..Fm._m9vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m9vC <- Fq..Fm._m9vC + xlab("Days After Stress") + ggtitle("CSHL20 F2b vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m9vC

ChlIdx_m9vC <- ggplot(data = m9_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m9vC <- ChlIdx_m9vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m9vC <- ChlIdx_m9vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m9vC <- ChlIdx_m9vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m9vC <- ChlIdx_m9vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m9vC <- ChlIdx_m9vC + xlab("Days After Stress") + ggtitle("CSHL20 F2b vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m9vC

AriIdx_m9vC <- ggplot(data = m9_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m9vC <- AriIdx_m9vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m9vC <- AriIdx_m9vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m9vC <- AriIdx_m9vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m9vC <- AriIdx_m9vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m9vC <- AriIdx_m9vC + xlab("Days After Stress") + ggtitle("CSHL20 F2b vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m9vC

NDVI_m9vC <- ggplot(data = m9_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m9vC <- NDVI_m9vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m9vC <- NDVI_m9vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m9vC <- NDVI_m9vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m9vC <- NDVI_m9vC + scale_color_manual(values = c("blue", "red"))
NDVI_m9vC <- NDVI_m9vC + xlab("Days After Stress") + ggtitle("CSHL20 F2b vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m9vC

Roimask_m10vC <- ggplot(data = m10_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m10vC <- Roimask_m10vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m10vC <- Roimask_m10vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m10vC <- Roimask_m10vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m10vC <- Roimask_m10vC + scale_color_manual(values = c("blue", "red"))
Roimask_m10vC <- Roimask_m10vC + xlab("Days After Stress") + ggtitle("CSHL21 L2c vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m10vC

Fq..Fm._m10vC <- ggplot(data = m10_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m10vC <- Fq..Fm._m10vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m10vC <- Fq..Fm._m10vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m10vC <- Fq..Fm._m10vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m10vC <- Fq..Fm._m10vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m10vC <- Fq..Fm._m10vC + xlab("Days After Stress") + ggtitle("CSHL21 L2c vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m10vC

ChlIdx_m10vC <- ggplot(data = m10_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m10vC <- ChlIdx_m10vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m10vC <- ChlIdx_m10vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m10vC <- ChlIdx_m10vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m10vC <- ChlIdx_m10vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m10vC <- ChlIdx_m10vC + xlab("Days After Stress") + ggtitle("CSHL21 L2c vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m10vC

AriIdx_m10vC <- ggplot(data = m10_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m10vC <- AriIdx_m10vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m10vC <- AriIdx_m10vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m10vC <- AriIdx_m10vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m10vC <- AriIdx_m10vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m10vC <- AriIdx_m10vC + xlab("Days After Stress") + ggtitle("CSHL21 L2c vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m10vC

NDVI_m10vC <- ggplot(data = m10_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m10vC <- NDVI_m10vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m10vC <- NDVI_m10vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m10vC <- NDVI_m10vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m10vC <- NDVI_m10vC + scale_color_manual(values = c("blue", "red"))
NDVI_m10vC <- NDVI_m10vC + xlab("Days After Stress") + ggtitle("CSHL21 L2c vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m10vC

Roimask_m11vC <- ggplot(data = m11_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m11vC <- Roimask_m11vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m11vC <- Roimask_m11vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m11vC <- Roimask_m11vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m11vC <- Roimask_m11vC + scale_color_manual(values = c("blue", "red"))
Roimask_m11vC <- Roimask_m11vC + xlab("Days After Stress") + ggtitle("CSHL22 F1c vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m11vC

Fq..Fm._m11vC <- ggplot(data = m11_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m11vC <- Fq..Fm._m11vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m11vC <- Fq..Fm._m11vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m11vC <- Fq..Fm._m11vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m11vC <- Fq..Fm._m11vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m11vC <- Fq..Fm._m11vC + xlab("Days After Stress") + ggtitle("CSHL22 F1c vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m11vC

ChlIdx_m11vC <- ggplot(data = m11_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m11vC <- ChlIdx_m11vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m11vC <- ChlIdx_m11vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m11vC <- ChlIdx_m11vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m11vC <- ChlIdx_m11vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m11vC <- ChlIdx_m11vC + xlab("Days After Stress") + ggtitle("CSHL22 F1c vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m11vC

AriIdx_m11vC <- ggplot(data = m11_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m11vC <- AriIdx_m11vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m11vC <- AriIdx_m11vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m11vC <- AriIdx_m11vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m11vC <- AriIdx_m11vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m11vC <- AriIdx_m11vC + xlab("Days After Stress") + ggtitle("CSHL22 F1c vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m11vC

NDVI_m11vC <- ggplot(data = m11_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m11vC <- NDVI_m11vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m11vC <- NDVI_m11vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m11vC <- NDVI_m11vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m11vC <- NDVI_m11vC + scale_color_manual(values = c("blue", "red"))
NDVI_m11vC <- NDVI_m11vC + xlab("Days After Stress") + ggtitle("CSHL22 F1c vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m11vC

Roimask_m12vC <- ggplot(data = m12_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m12vC <- Roimask_m12vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m12vC <- Roimask_m12vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m12vC <- Roimask_m12vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m12vC <- Roimask_m12vC + scale_color_manual(values = c("blue", "red"))
Roimask_m12vC <- Roimask_m12vC + xlab("Days After Stress") + ggtitle("WRKY vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m12vC

Fq..Fm._m12vC <- ggplot(data = m12_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m12vC <- Fq..Fm._m12vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m12vC <- Fq..Fm._m12vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m12vC <- Fq..Fm._m12vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m12vC <- Fq..Fm._m12vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m12vC <- Fq..Fm._m12vC + xlab("Days After Stress") + ggtitle("WRKY vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m12vC

ChlIdx_m12vC <- ggplot(data = m12_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m12vC <- ChlIdx_m12vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m12vC <- ChlIdx_m12vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m12vC <- ChlIdx_m12vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m12vC <- ChlIdx_m12vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m12vC <- ChlIdx_m12vC + xlab("Days After Stress") + ggtitle("WRKY vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m12vC

AriIdx_m12vC <- ggplot(data = m12_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m12vC <- AriIdx_m12vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m12vC <- AriIdx_m12vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m12vC <- AriIdx_m12vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m12vC <- AriIdx_m12vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m12vC <- AriIdx_m12vC + xlab("Days After Stress") + ggtitle("WRKY vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m12vC

NDVI_m12vC <- ggplot(data = m12_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m12vC <- NDVI_m12vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m12vC <- NDVI_m12vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m12vC <- NDVI_m12vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m12vC <- NDVI_m12vC + scale_color_manual(values = c("blue", "red"))
NDVI_m12vC <- NDVI_m12vC + xlab("Days After Stress") + ggtitle("WRKY vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m12vC

Roimask_m13vC <- ggplot(data = m13_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m13vC <- Roimask_m13vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m13vC <- Roimask_m13vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m13vC <- Roimask_m13vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m13vC <- Roimask_m13vC + scale_color_manual(values = c("blue", "red"))
Roimask_m13vC <- Roimask_m13vC + xlab("Days After Stress") + ggtitle("duf-5 vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m13vC

Fq..Fm._m13vC <- ggplot(data = m13_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m13vC <- Fq..Fm._m13vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m13vC <- Fq..Fm._m13vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m13vC <- Fq..Fm._m13vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m13vC <- Fq..Fm._m13vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m13vC <- Fq..Fm._m13vC + xlab("Days After Stress") + ggtitle("duf-5 vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m13vC

ChlIdx_m13vC <- ggplot(data = m13_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m13vC <- ChlIdx_m13vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m13vC <- ChlIdx_m13vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m13vC <- ChlIdx_m13vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m13vC <- ChlIdx_m13vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m13vC <- ChlIdx_m13vC + xlab("Days After Stress") + ggtitle("duf-5 vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m13vC

AriIdx_m13vC <- ggplot(data = m13_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m13vC <- AriIdx_m13vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m13vC <- AriIdx_m13vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m13vC <- AriIdx_m13vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m13vC <- AriIdx_m13vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m13vC <- AriIdx_m13vC + xlab("Days After Stress") + ggtitle("duf-5 vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m13vC

NDVI_m13vC <- ggplot(data = m13_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m13vC <- NDVI_m13vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m13vC <- NDVI_m13vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m13vC <- NDVI_m13vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m13vC <- NDVI_m13vC + scale_color_manual(values = c("blue", "red"))
NDVI_m13vC <- NDVI_m13vC + xlab("Days After Stress") + ggtitle("duf-5 vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m13vC

Roimask_m14vC <- ggplot(data = m14_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m14vC <- Roimask_m14vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m14vC <- Roimask_m14vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m14vC <- Roimask_m14vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m14vC <- Roimask_m14vC + scale_color_manual(values = c("blue", "red"))
Roimask_m14vC <- Roimask_m14vC + xlab("Days After Stress") + ggtitle("2xD vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m14vC

Fq..Fm._m14vC <- ggplot(data = m14_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m14vC <- Fq..Fm._m14vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m14vC <- Fq..Fm._m14vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m14vC <- Fq..Fm._m14vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m14vC <- Fq..Fm._m14vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m14vC <- Fq..Fm._m14vC + xlab("Days After Stress") + ggtitle("2xD vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m14vC

ChlIdx_m14vC <- ggplot(data = m14_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m14vC <- ChlIdx_m14vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m14vC <- ChlIdx_m14vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m14vC <- ChlIdx_m14vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m14vC <- ChlIdx_m14vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m14vC <- ChlIdx_m14vC + xlab("Days After Stress") + ggtitle("2xD vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m14vC

AriIdx_m14vC <- ggplot(data = m14_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m14vC <- AriIdx_m14vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m14vC <- AriIdx_m14vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m14vC <- AriIdx_m14vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m14vC <- AriIdx_m14vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m14vC <- AriIdx_m14vC + xlab("Days After Stress") + ggtitle("2xD vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m14vC

NDVI_m14vC <- ggplot(data = m14_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m14vC <- NDVI_m14vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m14vC <- NDVI_m14vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m14vC <- NDVI_m14vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m14vC <- NDVI_m14vC + scale_color_manual(values = c("blue", "red"))
NDVI_m14vC <- NDVI_m14vC + xlab("Days After Stress") + ggtitle("2xD vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m14vC

Roimask_m15vC <- ggplot(data = m15_v_C, aes(x = DOE, y = Roi.Mask, color = mutant, group = POT)) + theme_classic()
Roimask_m15vC <- Roimask_m15vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Roimask_m15vC <- Roimask_m15vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Roimask_m15vC <- Roimask_m15vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Roimask_m15vC <- Roimask_m15vC + scale_color_manual(values = c("blue", "red"))
Roimask_m15vC <- Roimask_m15vC + xlab("Days After Stress") + ggtitle("2xE vs Col-0 - Roi.mask over time") + theme(legend.position="bottom")
Roimask_m15vC

Fq..Fm._m15vC <- ggplot(data = m15_v_C, aes(x = DOE, y = Fq..Fm., color = mutant, group = POT)) + theme_classic()
Fq..Fm._m15vC <- Fq..Fm._m15vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
Fq..Fm._m15vC <- Fq..Fm._m15vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
Fq..Fm._m15vC <- Fq..Fm._m15vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
Fq..Fm._m15vC <- Fq..Fm._m15vC + scale_color_manual(values = c("blue", "red"))
Fq..Fm._m15vC <- Fq..Fm._m15vC + xlab("Days After Stress") + ggtitle("2xE vs Col-0 - Fq/Fm over time") + theme(legend.position="bottom")
Fq..Fm._m15vC

ChlIdx_m15vC <- ggplot(data = m15_v_C, aes(x = DOE, y = ChlIdx, color = mutant, group = POT)) + theme_classic()
ChlIdx_m15vC <- ChlIdx_m15vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
ChlIdx_m15vC <- ChlIdx_m15vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
ChlIdx_m15vC <- ChlIdx_m15vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
ChlIdx_m15vC <- ChlIdx_m15vC + scale_color_manual(values = c("blue", "red"))
ChlIdx_m15vC <- ChlIdx_m15vC + xlab("Days After Stress") + ggtitle("2xE vs Col-0 - ChlIdx over time") + theme(legend.position="bottom")
ChlIdx_m15vC

AriIdx_m15vC <- ggplot(data = m15_v_C, aes(x = DOE, y = AriIdx, color = mutant, group = POT)) + theme_classic()
AriIdx_m15vC <- AriIdx_m15vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
AriIdx_m15vC <- AriIdx_m15vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
AriIdx_m15vC <- AriIdx_m15vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
AriIdx_m15vC <- AriIdx_m15vC + scale_color_manual(values = c("blue", "red"))
AriIdx_m15vC <- AriIdx_m15vC + xlab("Days After Stress") + ggtitle("2xE vs Col-0 - AriIdx over time") + theme(legend.position="bottom")
AriIdx_m15vC

NDVI_m15vC <- ggplot(data = m15_v_C, aes(x = DOE, y = NDVI, color = mutant, group = POT)) + theme_classic()
NDVI_m15vC <- NDVI_m15vC + geom_line(alpha = 0.1) + facet_wrap(~treatment)
NDVI_m15vC <- NDVI_m15vC + stat_summary(fun.data = mean_se, geom = "ribbon", linetype = 0, aes(group = mutant), alpha = 0.3) + stat_summary(fun = mean, aes(group = mutant), size = 0.9, geom = "line", linetype = "solid")
NDVI_m15vC <- NDVI_m15vC + stat_compare_means(aes(group = mutant), label = "p.signif", method = "t.test", hide.ns = T)
NDVI_m15vC <- NDVI_m15vC + scale_color_manual(values = c("blue", "red"))
NDVI_m15vC <- NDVI_m15vC + xlab("Days After Stress") + ggtitle("2xE vs Col-0 - NDVI over time") + theme(legend.position="bottom")
NDVI_m15vC