20230921_RSA_LA1511_IAA_100mM_Salt_shoot_application_d9_only
This is root system architecture analysis and ICP-MS results for root of LA1511 treated on plate with or without salt. at d5 the seedlings were transferred to +/- salt, while their shoot that are exposed to outside of plates being sprayed +/- IAA for 5 days. after 10 days at salt, seedlings were harvested for ICPMS.and we only analyzed /traced RSA for d9. 3 replicates for each condition.
getwd()## [1] "C:/Users/Julkowska Lab/Desktop/R codes by Maryam/20230526_RSA_and _ICP-MS_for_LA1511_IAA_100mM_Salt_shoot_application_d9_only"list.files(pattern = ".csv")## [1] "d9-IAA-shoot-spray-root-corrected.csv"
## [2] "Eric06142023NaK-analyzed.csv"d9<-read.csv("d9-IAA-shoot-spray-root-corrected.csv")
d9$day <- 9
head(d9)Main_root <- subset(d9, d9$root_order == 0)
Main_rootcolnames(Main_root)## [1] "image" "root_name" "root"
## [4] "length" "vector_length" "surface"
## [7] "volume" "direction" "diameter"
## [10] "root_order" "root_ontology" "parent_name"
## [13] "parent" "insertion_position" "insertion_angle"
## [16] "n_child" "child_density" "first_child"
## [19] "insertion_first_child" "last_child" "insertion_last_child"
## [22] "day"MR_data <- Main_root[,c(1:4,10,16,17,19:22)]
MR_dataLateral_root <- subset(d9, d9$root_order != 0)
Lateral_rootunique(Lateral_root$root_order)## [1] 1MR_data_2 <- subset(MR_data, MR_data$n_child >0)temporary <- subset(Lateral_root, Lateral_root$parent == MR_data_2$root[1])
temporarytemporary <- subset(temporary, temporary$day == MR_data_2$day[3])
temporarydim(temporary)## [1] 27 22dim(temporary)[1]## [1] 27dim(temporary)[2]## [1] 22total_LRL <- sum(temporary$length)
LR_number <- dim(temporary)[1]
total_LRL## [1] 32.21086LR_number## [1] 27MR_data_2$LRL <- 0
MR_data_2$LRno <- 0
MR_data_2MR_data_2$LRL[1] <- total_LRL
MR_data_2$LRno[1] <- LR_number
MR_data_2MR_data_noChild <- subset(MR_data, MR_data$n_child == 0)
MR_data_noChildlength(MR_data_2$root)## [1] 18for(i in 2:18){
temporary <- subset(Lateral_root, Lateral_root$parent == MR_data_2$root[i])
temporary <- subset(temporary, temporary$day == MR_data_2$day[i])
total_LRL <- sum(temporary$length)
LR_number <- dim(temporary)[1]
MR_data_2$LRL[i] <- total_LRL
MR_data_2$LRno[i] <- LR_number
}
MR_data_2$check <- MR_data_2$n_child - MR_data_2$LRno
MR_data_2unique(MR_data_2$check)## [1] 0 2MR_data_Child2 <- MR_data_2[,1:13]
MR_data_Child2MR_data_Child2$root_name[10]## [1] " LA-S-MOCK"text <- strsplit(x = MR_data_Child2$root_name[10], split = "-")
text## [[1]]
## [1] " LA" "S" "MOCK"genotype <- text[[1]][1]
genotype <- gsub(" ", "", genotype)
genotype## [1] "LA"cond <- text[[1]][2:3]
cond## [1] "S" "MOCK"dim(MR_data_Child2)## [1] 18 13for(i in 1:18){
text <- strsplit(x = MR_data_Child2$root_name[i], split = "-")
genotype <- text[[1]][1]
cond <- paste(text[[1]][2], text[[1]][3], sep="_")
MR_data_Child2$genotype[i] <- genotype
MR_data_Child2$condition[i] <- cond
}
MR_data_Child2MR_data_Child2$TRS <- MR_data_Child2$length + MR_data_Child2$LRL
for(i in 1:nrow(MR_data_Child2)){
if(MR_data_Child2$LRno[i] == 0){
MR_data_Child2$aLRL[i] <- 0
} else {
MR_data_Child2$aLRL[i] <- MR_data_Child2$LRL[i]/ MR_data_Child2$LRno[i]
}
}
MR_data_Child2$MRpLRL <- MR_data_Child2$length / MR_data_Child2$LRL
MR_data_Child2length(unique(MR_data_Child2$root_name))## [1] 7unique(MR_data_Child2$day)## [1] 918/7## [1] 2.571429unique(MR_data_Child2$root_name)## [1] " LA-C-IAA"
## [2] " LA-S-IAA"
## [3] " LA-C-MOCK "
## [4] " LA-C-MOCK"
## [5] " LA-S-MOCK"
## [6] " LA-C-ONLY"
## [7] " LA-S-ONLY"unique(MR_data_Child2$genotype)## [1] " LA"MR_data_Child2$genotype <- gsub( " ", "", MR_data_Child2$genotype)
MR_data_Child2$root_name <- gsub( " ", "", MR_data_Child2$root_name)good_stuff <- c("LA")
funk <- subset(MR_data_Child2, !(MR_data_Child2$genotype %in% good_stuff))
funkgood_stuff2<- c("C-ONLY", "C-MOCK", "C-IAA", "S-ONLY" ,"S-MOCK" , "S-IAA")
funk2 <- subset(MR_data_Child2, !(MR_data_Child2$condition %in% good_stuff2))
funkunique(MR_data_Child2$genotype)## [1] "LA"unique(MR_data_Child2$condition)## [1] "C_IAA" "S_IAA"
## [3] "C_MOCK " "C_MOCK"
## [5] "S_MOCK" "C_ONLY"
## [7] "S_ONLY"unique(MR_data_Child2$condition)## [1] "C_IAA" "S_IAA"
## [3] "C_MOCK " "C_MOCK"
## [5] "S_MOCK" "C_ONLY"
## [7] "S_ONLY"MR_data_Child2$condition <- gsub( "C_MOCK ", "C_MOCK" , MR_data_Child2$condition)
MR_data_Child2$root_name <- gsub( "C_MOCK ", "C_MOCK", MR_data_Child2$root_name)
unique(MR_data_Child2$condition)## [1] "C_IAA" "S_IAA" "C_MOCK" "S_MOCK" "C_ONLY" "S_ONLY"library(ggplot2)
library(ggpubr)
MR_data_Child2$condition<- factor(MR_data_Child2$condition, levels=c("C_ONLY", "C_MOCK", "C_IAA", "S_ONLY", "S_MOCK", "S_IAA"))
histogram_TRS_IAA_SH <- ggdensity(MR_data_Child2, x = "TRS",
add = "mean", rug = TRUE, facet.by = "day",
color = "condition", fill = "condition")
histogram_TRS_IAA_SH
histogram_LRno_IAA_SH <- ggdensity(MR_data_Child2, x = "LRno",
add = "mean", rug = TRUE, facet.by = "day",
color = "condition", fill = "condition")
histogram_LRno_IAA_SH
TRS_graph <- ggerrorplot(MR_data_Child2, y = "TRS", x = "condition", fill="condition", color="condition",
desc_stat = "mean_sd", add = "jitter", facet.by = "genotype", palette = "jco",
add.params = list(color = "darkgray"),
xlab="", ylab="Total Root Size (cm)")
TRS_graph<- TRS_graph + rremove("legend") + stat_compare_means(method="t.test", ref.group = "C_ONLY",
label = "p.signif", hide.ns = T)
TRS_graph <- TRS_graph + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
TRS_graph
MR_graph <- ggerrorplot(MR_data_Child2, y = "length", x = "condition", fill="condition", color="condition",
desc_stat = "mean_sd", add = "jitter", facet.by = "genotype", palette = "jco",
add.params = list(color = "darkgray"),
xlab="", ylab="Main Root Length (cm)")
MR_graph<- MR_graph + rremove("legend") + stat_compare_means(method="t.test", ref.group = "C_ONLY",
label = "p.signif", hide.ns = T)
MR_graph <- MR_graph + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
MR_graph
LRno_graph <- ggerrorplot(MR_data_Child2, y = "LRno", x = "condition", fill="condition", color="condition",
desc_stat = "mean_sd", add = "jitter", facet.by = "genotype", palette = "jco",
add.params = list(color = "darkgray"),
xlab="", ylab="Lateral root number")
LRno_graph<- LRno_graph + rremove("legend") + stat_compare_means(method="t.test", ref.group = "C_ONLY",
label = "p.signif", hide.ns = T)
LRno_graph <- LRno_graph + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
LRno_graph
LRL_graph <- ggerrorplot(MR_data_Child2, y = "LRL", x = "condition", fill="condition", color="condition",
desc_stat = "mean_sd", add = "jitter", facet.by = "genotype", palette = "jco",
add.params = list(color = "darkgray"),
xlab="", ylab="Lateral root length (cm)")
LRL_graph<- LRL_graph + rremove("legend") + stat_compare_means(method="t.test", ref.group = "C_ONLY",
label = "p.signif", hide.ns = T)
LRL_graph <- LRL_graph + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
LRL_graph
aLRL_graph <- ggerrorplot(MR_data_Child2, y = "aLRL", x = "condition", fill="condition", color="condition",
desc_stat = "mean_sd", add = "jitter", facet.by = "genotype", palette = "jco",
add.params = list(color = "darkgray"),
xlab="", ylab="Average lateral root length (cm)")
aLRL_graph<- aLRL_graph + rremove("legend") + stat_compare_means(method="t.test", ref.group = "C_ONLY",
label = "p.signif", hide.ns = T)
aLRL_graph <- aLRL_graph + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
aLRL_graph