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getwd()
## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/202311_Tomato_shoot_growth_ACC_la_248_salt_soil"
my_files <- list.files(pattern = ".csv")
my_files
## [1] "FW_lastday_ACC_salt_soil.csv"
## [2] "Maryam_2tomatoes_ACC_salt_soil_data.csv"
## [3] "Results_110823.csv"
## [4] "Results_110823_half_deleted.csv"
## [5] "Results_111423.csv"
## [6] "Results_111623.csv"
## [7] "Results_112123.csv"
d10<-read.csv("Results_110823_half_deleted.csv")
d16<-read.csv("Results_111423.csv")
d18<-read.csv("Results_111623.csv")
d23<-read.csv("Results_112123.csv")
#lets add days of stress here
d10$day <- 10
d16$day <- 16
d18$day <- 18
d23$day <- 23
d23
#install.packages("doBy")
library(doBy)
sum_data_d23 <- summaryBy(Area + Height + Width ~ Accession + condition + Pot_no, data = d23, FUN = function(x) c(mean = mean(x), sum=sum(x), max=max(x)))
sum_data_d23$day <- 23
sum_data_d23
sum_data_d18 <- summaryBy(Area + Height + Width ~ Accession + condition + Pot_no, data = d18, FUN = function(x) c(mean = mean(x), sum=sum(x), max=max(x)))
sum_data_d18$day <- 18
sum_data_d18
sum_data_d16 <- summaryBy(Area + Height + Width ~ Accession + condition + Pot_no, data = d16, FUN = function(x) c(mean = mean(x), sum=sum(x), max=max(x)))
sum_data_d16$day <- 16
sum_data_d16
sum_data_d10 <- summaryBy(Area + Height + Width ~ Accession + condition + Pot_no, data = d10, FUN = function(x) c(mean = mean(x), sum=sum(x), max=max(x)))
sum_data_d10$day <- 10
sum_data_d10
all_data <- rbind(sum_data_d10, sum_data_d16)
all_data <- rbind(all_data, sum_data_d18)
all_data <- rbind(all_data,sum_data_d23)
all_data
library(ggplot2)
library(ggpubr)
library("ggsci")
all_data$cond1 <- strsplit(all_data$condition, "-")
unique(all_data$cond1)
## [[1]]
## [1] "c" "acc"
##
## [[2]]
## [1] "c" "mock"
##
## [[3]]
## [1] "c" "noacc"
##
## [[4]]
## [1] "s" "acc"
##
## [[5]]
## [1] "s" "mock"
##
## [[6]]
## [1] "s" "noacc"
for(i in 1:nrow(all_data)){
all_data$Salt[i] <- all_data$cond1[[i]][1]
all_data$Acc[i] <- all_data$cond1[[i]][2]
}
head(all_data)
Area_graph <- ggplot(data=all_data, aes(x= day, y=Area.sum, group = Pot_no, color = Acc))
Area_graph <- Area_graph + geom_line(alpha = 0.5) + facet_wrap(~ Salt)
Area_graph <- Area_graph + stat_summary(fun.data = mean_se, geom="ribbon", linetype=0, aes(group= Acc), alpha=0.3)
Area_graph <- Area_graph + stat_summary(fun=mean, aes(group= Acc), size=0.7, geom="line", linetype = "dashed")
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
Area_graph <- Area_graph + stat_compare_means(aes(group = Acc), label = "p.signif", method = "aov", hide.ns = T)
Area_graph <- Area_graph + ylab("Shoot Size (7 x SV pixels)") + xlab("Days After Stress") + scale_color_jco()
Area_graph
#Let’s save the data too into a csv file:
#write.csv(all_data, "Maryam_2tomatoes_ACC_salt_soil_data.csv", row.names = FALSE)
all_data2 <- all_data
mock_sub <- subset(all_data2, all_data2$Acc %in% c("acc", "mock"))
mock_sub
noacc_sub <- subset(all_data2, all_data2$Acc %in% c("acc", "noacc"))
noacc_sub
mock_sub$compare <- "mock"
noacc_sub$compare <- "noacc"
all_data3 <- rbind(mock_sub, noacc_sub)
Area_graph_2way <- ggplot(data=all_data3, aes(x= day, y=Area.sum, group = Pot_no, color = Acc))
Area_graph_2way <- Area_graph_2way + geom_line(alpha = 0.5) + facet_wrap(compare ~ Salt)
Area_graph_2way <- Area_graph_2way + stat_summary(fun.data = mean_se, geom="ribbon", linetype=0, aes(group= Acc), alpha=0.3)
Area_graph_2way <- Area_graph_2way + stat_summary(fun=mean, aes(group= Acc), size=0.7, geom="line", linetype = "dashed")
Area_graph_2way <- Area_graph_2way + stat_compare_means(aes(group = Acc), label = "p.signif", method = "aov", hide.ns = T)
Area_graph_2way <- Area_graph_2way + ylab("Shoot Size (7 x SV pixels)") + xlab("Days After Stress") + scale_color_jco()
Area_graph_2way
Area_graph_accession <- ggplot(data=all_data, aes(x= day, y=Area.sum, group = Accession, color = condition))
Area_graph_accession <- Area_graph_accession + geom_line(alpha = 0.1) + facet_wrap(~ Accession)
Area_graph_accession <- Area_graph_accession + stat_summary(fun.data = mean_se, geom="ribbon", linetype=0, aes(group= condition), alpha=0.3)
Area_graph_accession <- Area_graph_accession + stat_summary(fun=mean, aes(group= condition), size=0.7, geom="line", linetype = "dashed")
Area_graph_accession <- Area_graph_accession + stat_compare_means(aes(group = condition), label = "p.signif", method = "t.test", hide.ns = T)
Area_graph_accession <- Area_graph_accession + ylab("Shoot Size (7 x SV pixels)") + xlab("Days After Stress") + scale_color_aaas()
Area_graph_accession
FW_ACC <- read.csv("FW_lastday_ACC_salt_soil.csv")
FW_ACC
last_day <- subset(all_data, all_data$day == 23)
last_day
#LETS merge FW data with digital growth data on last day
last_day_FW <- merge(last_day, FW_ACC, by=c( "Accession", "condition"), all=TRUE)
last_day_FW
unique(last_day_FW$condition)
## [1] "c-acc" "c-mock" "c-noacc" "s-acc" "s-mock" "s-noacc"
last_day_c_acc <- subset(last_day_FW, last_day_FW$condition == "c-acc")
last_day_c_mock <- subset(last_day_FW, last_day_FW$condition == "c-mock")
last_day_c_noacc <- subset(last_day_FW, last_day_FW$condition == "c-noacc")
last_day_s_acc <- subset(last_day_FW, last_day_FW$condition == "s-acc")
last_day_s_mock <- subset(last_day_FW, last_day_FW$condition == "s-mock")
last_day_s_noacc <- subset(last_day_FW, last_day_FW$condition == "s-noacc")
FW_Area_c_acc <- ggscatter(last_day_c_acc, x = "Area.sum", y = "Total.FW.g.20231127.4weeks",rug = TRUE) + stat_cor()
FW_Area_c_acc
FW_Area_c_mock <- ggscatter(last_day_c_mock, x = "Area.sum", y = "Total.FW.g.20231127.4weeks",rug = TRUE) + stat_cor()
FW_Area_c_mock
FW_Area_c_noacc <- ggscatter(last_day_c_noacc, x = "Area.sum", y = "Total.FW.g.20231127.4weeks",rug = TRUE) + stat_cor()
FW_Area_c_noacc
FW_Area_s_acc <- ggscatter(last_day_s_acc, x = "Area.sum", y = "Total.FW.g.20231127.4weeks",rug = TRUE) + stat_cor()
FW_Area_s_acc
FW_Area_s_mock <- ggscatter(last_day_s_mock, x = "Area.sum", y = "Total.FW.g.20231127.4weeks",rug = TRUE) + stat_cor()
FW_Area_s_mock
FW_Area_s_noacc <- ggscatter(last_day_s_noacc, x = "Area.sum", y = "Total.FW.g.20231127.4weeks",rug = TRUE) + stat_cor()
FW_Area_s_noacc