R Notebook

Analysis of PhotosynQ data from aeroponics drought simulation test performed 2024/06/04-2024/06/18. PhotosynQ measurements were taken every day, for the most part. We used two accessions, UCR779 and Suvita2. Drought treatment had misters on for 2 minutes then off for 20 minutes, while control had misters on for 2 minutes and off for 5 minutes.

#load libraries
library("ggplot2")
library("cowplot")
library("ggpubr")

getwd()

[1] "C:/Users/J Lab/Desktop"

list.files(pattern=".csv")

[1] "aero_drought_sim_20240621.csv" "drought simulation FW_DW.csv" 

PhotosynQ <- read.csv("aero_drought_sim_20240621.csv")
PhotosynQ

colnames(PhotosynQ)

 [1] "ID"                            "Series"                        "Repeat"                        "Accession"                    
 [5] "Rep"                           "Condition"                     "air_temp_kinetics"             "Ambient.Humidity"             
 [9] "Ambient.Pressure"              "Ambient.Temperature"           "data_raw_PAM"                  "ECS_averaged_trace"           
[13] "ECS_tau"                       "ECSt.mAU"                      "fitinput"                      "FmPrime"                      
[17] "FoPrime"                       "Fs"                            "FvP_over_FmP"                  "gH."                          
[21] "humidity2_K"                   "humidity_K"                    "kP700"                         "leaf.angle"                   
[25] "Leaf.Temperature"              "Leaf.Temperature.Differenial"  "Leaf.Temperature.Differential" "LEAF_temp"                    
[29] "leaf_thickness"                "LEF"                           "LEFd_trace"                    "Light.Intensity..PAR."        
[33] "NPQt"                          "outdata"                       "P700_DIRK_ampl"                "P700_DIRK_averaged_trace"     
[37] "P700_fitinput"                 "P700_outdata"                  "Phi2"                          "PhiNO"                        
[41] "PhiNPQ"                        "PS1.Active.Centers"            "PS1.Open.Centers"              "PS1.Over.Reduced.Centers"     
[45] "PS1.Oxidized.Centers"          "PSI_data_absorbance"           "pump"                          "qL"                           
[49] "SPAD"                          "test_data_raw_PAM"             "day"                           "time"                         
[53] "time2"                         "tP700"                         "v_initial_P700"                "vH."                          
[57] "User"                          "Device.ID"                     "Latitude"                      "Longitude"                    
[61] "Issues"                       

#we are interested in: Condition, Rep, Accession, FoPrime, PhiNPQ, FvP_over_FmP, FmPrime, PS1.Active.Centers, PS1.Open.Centers, PS1.Over.Reduced.Centers, PS1.Oxidized.Centers, leaf_thickness, Leaf.Temperature, SPAD
PQ <- PhotosynQ[,c(4:6, 16:17, 19, 25, 29, 41:45, 49, 51)]
PQ

unique(PQ$day)

 [1] "6/18/2024 0:00" "6/17/2024 0:00" "6/13/2024 0:00" "6/11/2024 0:00" "6/10/2024 0:00" "6/9/2024 0:00"  "6/8/2024 0:00"  "6/7/2024 0:00" 
 [9] "6/6/2024 0:00"  "6/5/2024 0:00"  "6/4/2024 0:00" 

PQ$time <- as.factor(PQ$day)
PQ$day.of.stress <- PQ$day
PQ$day.of.stress <- gsub("6/4/2024 0:00", "0", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/5/2024 0:00", "1", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/6/2024 0:00", "2", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/7/2024 0:00", "3", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/8/2024 0:00", "4", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/9/2024 0:00", "5", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/10/2024 0:00", "6", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/11/2024 0:00", "7", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/13/2024 0:00", "9", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/17/2024 0:00", "13", PQ$day.of.stress)
PQ$day.of.stress <- gsub("6/18/2024 0:00", "14", PQ$day.of.stress)
colnames(PQ)

 [1] "Accession"                "Rep"                      "Condition"                "FmPrime"                  "FoPrime"                 
 [6] "FvP_over_FmP"             "Leaf.Temperature"         "leaf_thickness"           "PhiNPQ"                   "PS1.Active.Centers"      
[11] "PS1.Open.Centers"         "PS1.Over.Reduced.Centers" "PS1.Oxidized.Centers"     "SPAD"                     "day"                     
[16] "time"                     "day.of.stress"           

PQ <- PQ[,c(17, 1:14)]
PQ

PQ$Accession <- gsub("UCR", "UCR779", PQ$Accession)
PQ$Accession <- gsub("UCR779779", "UCR779", PQ$Accession)
PQ$Accession <- gsub("Suvita", "Suvita2", PQ$Accession)
PQ$Accession <- gsub("Suvita22", "Suvita2", PQ$Accession)
PQ$Accession <- gsub("suvita2", "Suvita2", PQ$Accession)
unique(PQ$Accession)

[1] "UCR779"  "Suvita2"

unique(PQ$Rep)

[1] 1 2

PQ$Plant.ID <- paste(PQ$Accession, PQ$Rep, PQ$Condition, sep="_")
PQ

##Facet by condition

PQ$Plant.ID <- as.factor(PQ$Plant.ID)

PQ$FmPrime <- as.numeric(as.character(PQ$FmPrime))
PQ

PQ$day.of.stress <- as.factor(as.character(PQ$day.of.stress))
PQ

FmP_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = FmPrime, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
FmP_over_time <- FmP_over_time + geom_line(alpha = 0.4)
FmP_over_time <- FmP_over_time + facet_wrap(~ Condition)
FmP_over_time <- FmP_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
FmP_over_time <- FmP_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
FmP_over_time <- FmP_over_time + ylab("FmPrime (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
FmP_over_time

PQ$FoPrime <- as.numeric(as.character(PQ$FoPrime))

FoP_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = FoPrime, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
FoP_over_time <- FoP_over_time + geom_line(alpha = 0.4)
FoP_over_time <- FoP_over_time + facet_wrap(~ Condition)
FoP_over_time <- FoP_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
FoP_over_time <- FoP_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
FoP_over_time <- FoP_over_time + ylab("FoPrime (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
FoP_over_time

PQ$FvP_over_FmP <- as.numeric(as.character(PQ$FvP_over_FmP))

FvP_over_FmP_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = FvP_over_FmP, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
FvP_over_FmP_over_time <- FvP_over_FmP_over_time + geom_line(alpha = 0.4)
FvP_over_FmP_over_time <- FvP_over_FmP_over_time + facet_wrap(~ Condition)
FvP_over_FmP_over_time <- FvP_over_FmP_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
FvP_over_FmP_over_time <- FvP_over_FmP_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
FvP_over_FmP_over_time <- FvP_over_FmP_over_time + ylab("FvP_over_FmP (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
FvP_over_FmP_over_time

PQ$Leaf.Temperature <- as.numeric(as.character(PQ$Leaf.Temperature))

Leaf_temp_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = Leaf.Temperature, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
Leaf_temp_over_time <- Leaf_temp_over_time + geom_line(alpha = 0.4)
Leaf_temp_over_time <- Leaf_temp_over_time + facet_wrap(~ Condition)
Leaf_temp_over_time <- Leaf_temp_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
Leaf_temp_over_time <- Leaf_temp_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
Leaf_temp_over_time <- Leaf_temp_over_time + ylab("Leaf temperature (C)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
Leaf_temp_over_time

PQ$leaf_thickness <- as.numeric(as.character(PQ$leaf_thickness))

Leaf_thickness_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = leaf_thickness, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
Leaf_thickness_over_time <- Leaf_thickness_over_time + geom_line(alpha = 0.4)
Leaf_thickness_over_time <- Leaf_thickness_over_time + facet_wrap(~ Condition)
Leaf_thickness_over_time <- Leaf_thickness_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
Leaf_thickness_over_time <- Leaf_thickness_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
Leaf_thickness_over_time <- Leaf_thickness_over_time + ylab("Leaf_thickness (mm)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
Leaf_thickness_over_time

PQ$PhiNPQ <- as.numeric(as.character(PQ$PhiNPQ))

PhiNPQ_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = PhiNPQ, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
PhiNPQ_over_time <- PhiNPQ_over_time + geom_line(alpha = 0.4)
PhiNPQ_over_time <- PhiNPQ_over_time + facet_wrap(~ Condition)
PhiNPQ_over_time <- PhiNPQ_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
PhiNPQ_over_time <- PhiNPQ_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
PhiNPQ_over_time <- PhiNPQ_over_time + ylab("PhiNPQ (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
PhiNPQ_over_time

PQ$PS1.Active.Centers <- as.numeric(as.character(PQ$PS1.Active.Centers))

PS1_active_centers_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Active.Centers, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
PS1_active_centers_over_time <- PS1_active_centers_over_time + geom_line(alpha = 0.4)
PS1_active_centers_over_time <- PS1_active_centers_over_time + facet_wrap(~ Condition)
PS1_active_centers_over_time <- PS1_active_centers_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
PS1_active_centers_over_time <- PS1_active_centers_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
PS1_active_centers_over_time <- PS1_active_centers_over_time + ylab("PS1 Active Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
PS1_active_centers_over_time

PQ$PS1.Open.Centers <- as.numeric(as.character(PQ$PS1.Open.Centers))

PS1_Open_Centers_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Open.Centers, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic() + ylim(0, NA)
PS1_Open_Centers_over_time <- PS1_Open_Centers_over_time + geom_line(alpha = 0.4)
PS1_Open_Centers_over_time <- PS1_Open_Centers_over_time + facet_wrap(~ Condition)
PS1_Open_Centers_over_time <- PS1_Open_Centers_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
PS1_Open_Centers_over_time <- PS1_Open_Centers_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
PS1_Open_Centers_over_time <- PS1_Open_Centers_over_time + ylab("PS1 Open Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
PS1_Open_Centers_over_time

PQ$PS1.Over.Reduced.Centers <- as.numeric(as.character(PQ$PS1.Over.Reduced.Centers))

PS1_Over_Reduced.Centers_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Over.Reduced.Centers, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic()
PS1_Over_Reduced.Centers_over_time <- PS1_Over_Reduced.Centers_over_time + geom_line(alpha = 0.4)
PS1_Over_Reduced.Centers_over_time <- PS1_Over_Reduced.Centers_over_time + facet_wrap(~ Condition)
PS1_Over_Reduced.Centers_over_time <- PS1_Over_Reduced.Centers_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
PS1_Over_Reduced.Centers_over_time <- PS1_Over_Reduced.Centers_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
PS1_Over_Reduced.Centers_over_time <- PS1_Over_Reduced.Centers_over_time + ylab("PS1 Over Reduced Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
PS1_Over_Reduced.Centers_over_time

PQ$PS1.Oxidized.Centers <- as.numeric(as.character(PQ$PS1.Oxidized.Centers))

PS1_Oxidized_Centers_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Oxidized.Centers, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic()
PS1_Oxidized_Centers_over_time <- PS1_Oxidized_Centers_over_time + geom_line(alpha = 0.4)
PS1_Oxidized_Centers_over_time <- PS1_Oxidized_Centers_over_time + facet_wrap(~ Condition)
PS1_Oxidized_Centers_over_time <- PS1_Oxidized_Centers_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
PS1_Oxidized_Centers_over_time <- PS1_Oxidized_Centers_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
PS1_Oxidized_Centers_over_time <- PS1_Oxidized_Centers_over_time + ylab("PS1 Oxidized Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
PS1_Oxidized_Centers_over_time

PQ$SPAD <- as.numeric(as.character(PQ$SPAD))

SPAD_over_time <- ggplot(data = PQ, aes(x = day.of.stress, y = SPAD, group = Plant.ID, colour = Accession), na.rm = TRUE) + theme_classic()
SPAD_over_time <- SPAD_over_time + geom_line(alpha = 0.4)
SPAD_over_time <- SPAD_over_time + facet_wrap(~ Condition)
SPAD_over_time <- SPAD_over_time + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Accession), alpha = 0.3) + stat_summary(fun = mean, aes(group = Accession), linewidth = 0.7, geom = "line", linetype = "dashed")
SPAD_over_time <- SPAD_over_time + stat_compare_means(aes(group = Accession), label = "p.signif", method = "t.test", hide.ns = TRUE)
SPAD_over_time <- SPAD_over_time + ylab("SPAD (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
SPAD_over_time

##Facet by accession

FmP_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = FmPrime, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
FmP_by_acc <- FmP_by_acc + geom_line(alpha = 0.4)
FmP_by_acc <- FmP_by_acc + facet_wrap(~ Accession)
FmP_by_acc <- FmP_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
FmP_by_acc <- FmP_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
FmP_by_acc <- FmP_by_acc + ylab("FmPrime (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
FmP_by_acc

Fo_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = FoPrime, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
Fo_by_acc <- Fo_by_acc + geom_line(alpha = 0.4)
Fo_by_acc <- Fo_by_acc + facet_wrap(~ Accession)
Fo_by_acc <- Fo_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
Fo_by_acc <- Fo_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
Fo_by_acc <- Fo_by_acc + ylab("FoPrime (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
Fo_by_acc

FvPoverFmP_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = FvP_over_FmP, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
FvPoverFmP_by_acc <- FvPoverFmP_by_acc + geom_line(alpha = 0.4)
FvPoverFmP_by_acc <- FvPoverFmP_by_acc + facet_wrap(~ Accession)
FvPoverFmP_by_acc <- FvPoverFmP_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
FvPoverFmP_by_acc <- FvPoverFmP_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
FvPoverFmP_by_acc <- FvPoverFmP_by_acc + ylab("FvP_over_FmP (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
FvPoverFmP_by_acc

leaftemp_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = Leaf.Temperature, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
leaftemp_by_acc <- leaftemp_by_acc + geom_line(alpha = 0.4)
leaftemp_by_acc <- leaftemp_by_acc + facet_wrap(~ Accession)
leaftemp_by_acc <- leaftemp_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
leaftemp_by_acc <- leaftemp_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
leaftemp_by_acc <- leaftemp_by_acc + ylab("Leaf.Temperature (C)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
leaftemp_by_acc

leafthick_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = leaf_thickness, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
leafthick_by_acc <- leafthick_by_acc + geom_line(alpha = 0.4)
leafthick_by_acc <- leafthick_by_acc + facet_wrap(~ Accession)
leafthick_by_acc <- leafthick_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
leafthick_by_acc <- leafthick_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
leafthick_by_acc <- leafthick_by_acc + ylab("leaf_thickness (mm)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
leafthick_by_acc

PhiNPQ_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = PhiNPQ, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
PhiNPQ_by_acc <- PhiNPQ_by_acc + geom_line(alpha = 0.4)
PhiNPQ_by_acc <- PhiNPQ_by_acc + facet_wrap(~ Accession)
PhiNPQ_by_acc <- PhiNPQ_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
PhiNPQ_by_acc <- PhiNPQ_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
PhiNPQ_by_acc <- PhiNPQ_by_acc + ylab("PhiNPQ (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
PhiNPQ_by_acc

activecenters_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Active.Centers, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
activecenters_by_acc <- activecenters_by_acc + geom_line(alpha = 0.4)
activecenters_by_acc <- activecenters_by_acc + facet_wrap(~ Accession)
activecenters_by_acc <- activecenters_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
activecenters_by_acc <- activecenters_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
activecenters_by_acc <- activecenters_by_acc + ylab("PS1.Active.Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
activecenters_by_acc

opencenters_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Open.Centers, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
opencenters_by_acc <- opencenters_by_acc + geom_line(alpha = 0.4)
opencenters_by_acc <- opencenters_by_acc + facet_wrap(~ Accession)
opencenters_by_acc <- opencenters_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
opencenters_by_acc <- opencenters_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
opencenters_by_acc <- opencenters_by_acc + ylab("PS1.Open.Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
opencenters_by_acc

overreduced_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Over.Reduced.Centers, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic()
overreduced_by_acc <- overreduced_by_acc + geom_line(alpha = 0.4)
overreduced_by_acc <- overreduced_by_acc + facet_wrap(~ Accession)
overreduced_by_acc <- overreduced_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
overreduced_by_acc <- overreduced_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
overreduced_by_acc <- overreduced_by_acc + ylab("PS1.Over.Reduced.Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
overreduced_by_acc

oxidized_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = PS1.Oxidized.Centers, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic()
oxidized_by_acc <- oxidized_by_acc + geom_line(alpha = 0.4)
oxidized_by_acc <- oxidized_by_acc + facet_wrap(~ Accession)
oxidized_by_acc <- oxidized_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
oxidized_by_acc <- oxidized_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
oxidized_by_acc <- oxidized_by_acc + ylab("PS1.Oxidized.Centers (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
oxidized_by_acc

SPAD_by_acc <- ggplot(data = PQ, aes(x = day.of.stress, y = SPAD, group = Plant.ID, colour = Condition), na.rm = TRUE) + theme_classic() + ylim(0, NA)
SPAD_by_acc <- SPAD_by_acc + geom_line(alpha = 0.4)
SPAD_by_acc <- SPAD_by_acc + facet_wrap(~ Accession)
SPAD_by_acc <- SPAD_by_acc + stat_summary(fun.data = mean_se, linetype = 0, aes(group = Condition), alpha = 0.3) + stat_summary(fun = mean, aes(group = Condition), linewidth = 0.7, geom = "line", linetype = "dashed")
SPAD_by_acc <- SPAD_by_acc + stat_compare_means(aes(group = Condition), label = "p.signif", method = "t.test", hide.ns = TRUE)
SPAD_by_acc <- SPAD_by_acc + ylab("SPAD (a.u.)") + xlab("Day of Stress") + scale_color_manual(values=c("blue", "red"))
SPAD_by_acc

#save all as PDF

#facet condition
pdf("FmPrime_facet_condition.pdf", width = 10, height = 7)
plot(FmP_over_time)
dev.off()

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pdf("FoPrime_facet_condition.pdf", width = 10, height = 7)

plot(FoP_over_time)
dev.off()

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pdf("FvP_over_FmP_facet_condition.pdf", width = 10, height = 7)

plot(FvP_over_FmP_over_time)
dev.off()

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pdf("leaf_temp_facet_condition.pdf", width = 10, height = 7)

plot(Leaf_temp_over_time)
dev.off()

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pdf("leaf_thickness_facet_condition.pdf", width = 10, height = 7)

plot(Leaf_thickness_over_time)
dev.off()

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pdf("PhiNPQ_facet_condition.pdf", width = 10, height = 7)

plot(PhiNPQ_over_time)
dev.off()

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pdf("PS1_active_centers_facet_condition.pdf", width = 10, height = 7)

plot(PS1_active_centers_over_time)
dev.off()

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pdf("PS1_open_centers_facet_condition.pdf", width = 10, height = 7)

plot(PS1_Open_Centers_over_time)
dev.off()

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pdf("PS1_over_reduced_centers_facet_condition.pdf", width = 10, height = 7)

plot(PS1_Over_Reduced.Centers_over_time)
dev.off()

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pdf("PS1_oxidized_centers_facet_condition.pdf", width = 10, height = 7)

plot(PS1_Oxidized_Centers_over_time)
dev.off()

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pdf("SPAD_facet_condition.pdf", width = 10, height = 7)

plot(SPAD_over_time)
dev.off()

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#facet accession
pdf("FmPrime_facet_accession.pdf", width = 10, height = 7)
plot(FmP_by_acc)
dev.off()

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pdf("FoPrime_facet_accession.pdf", width = 10, height = 7)

plot(Fo_by_acc)
dev.off()

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pdf("FvP_over_FmP_facet_accession.pdf", width = 10, height = 7)

plot(FvPoverFmP_by_acc)
dev.off()

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pdf("leaf_temp_facet_accession.pdf", width = 10, height = 7)

plot(leaftemp_by_acc)
dev.off()

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pdf("leaf_thickness_facet_accession.pdf", width = 10, height = 7)

plot(leafthick_by_acc)
dev.off()

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pdf("PhiNPQ_facet_accession.pdf", width = 10, height = 7)

plot(PhiNPQ_by_acc)
dev.off()

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pdf("PS1_active_centers_facet_accession.pdf", width = 10, height = 7)

plot(activecenters_by_acc)
dev.off()

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pdf("PS1_open_centers_facet_accession.pdf", width = 10, height = 7)

plot(opencenters_by_acc)
dev.off()

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pdf("PS1_over_reduced_centers_facet_accession.pdf", width = 10, height = 7)

plot(overreduced_by_acc)
dev.off()

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pdf("PS1_oxidized_centers_facet_accession.pdf", width = 10, height = 7)

plot(oxidized_by_acc)
dev.off()

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pdf("SPAD_facet_accession.pdf", width = 10, height = 7)

plot(SPAD_by_acc)
dev.off()

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