Tox-path/Master Boxplot.R at main · elijahedmondson/Tox-path · GitHub

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library(gridExtra)
library(readxl)
library(ggpubr)
library(Rmisc)
library(tidyverse)
library(plyr)
library(GGally)
library(ggplot2)
library(tidyverse)
library(gapminder)
library(dplyr)
library(ggsignif)
library(dplyr)

setwd("C:/Users/edmondsonef/Desktop/R-plots/")
data <- read_excel("C:/Users/edmondsonef/Desktop/TMEM205/MHL 240253 TMEM205.xlsx", sheet = "New")

#data <- dplyr::filter(data, Sex == "M")
#data <- dplyr::filter(data, Group != "F08")


### Albulmin:Globulin Ratio
data<-dplyr:: mutate(data, AGR = (ALB/(TP-ALB)))
data<-dplyr:: mutate(data, BCR = (BUN/CRE))


names <- colnames(data)


# #for 1 levels
# plot_list = list(colnames(data))
# for(i in 10:length(colnames(data))){
#   theme_set(theme_bw(12))
#   plot_list[[i]] <- local ({
#     i <- i
#     variable = as.matrix(data[i])
#     y_title = colnames(data[i])
#     ggplot(data, aes(x = Groups, y = variable, color = Group)) +
#       geom_boxplot(outlier.shape=NA, show.legend = F) +
#       scale_y_continuous(name = y_title) +
#       theme(axis.title.x=element_blank()) +
#       geom_point(aes(color = Group),
#                  position=position_jitterdodge(dodge.width = 0.75, jitter.width = 0.003),
#                  size = 2)
#   })
# }


#for 2 levels
plot_list = list(colnames(data))
for(i in 15:length(colnames(data))){
  theme_set(theme_bw(12))
  plot_list[[i]] <- local ({
    i <- i
    variable = as.matrix(data[i])
    y_title = colnames(data[i])
    ggplot(data, aes(x = Treatment, y = variable, color = Genotype)) +
      geom_boxplot(outlier.shape=NA, show.legend = F) +
      scale_y_continuous(name = y_title) +
      theme(axis.title.x=element_blank()) +
      #theme(axis.text.x=element_text(angle=25,hjust=1)) +
      geom_point(aes(color = Genotype, shape = Sex),
                 position=position_jitterdodge(dodge.width = 0.75, jitter.width = 0.003),
                 size = 2)
  })
}


plot_list[[1]]

library(patchwork)
setwd("C:/Users/edmondsonef/Desktop/R-plots/")
tiff("CBC_WBC.tiff", units="in", width=8, height=8, res=200)
(plot_list[[49]] | plot_list[[50]]) /
  (plot_list[[51]]  | plot_list[[52]]) /
  (plot_list[[53]]  | plot_list[[54]]) /
  (plot_list[[63]]  | plot_list[[64]]) /
  plot_layout(guides = "collect") +
  plot_annotation(title = "CBC: White Blood Cell and Platelet Counts")
dev.off()

tiff("CBC_RBC.tiff", units="in", width=8, height=8, res=200)
(plot_list[[55]] | plot_list[[56]]) /
  (plot_list[[57]]  | plot_list[[58]]) /
  (plot_list[[59]]  | plot_list[[60]]) /
  (plot_list[[61]]  | plot_list[[62]]) /
  plot_layout(guides = "collect") +
  plot_annotation(title = "CBC: Erythroid Parameters")
dev.off()

tiff("Chemistry.tiff", units="in", width=14, height=12, res=200)
(plot_list[[43]] | plot_list[[31]] | plot_list[[44]] | plot_list[[66]]) /
  (plot_list[[36]] | plot_list[[39]] | plot_list[[67]] | plot_list[[40]]) /
  (plot_list[[37]] | plot_list[[38]] | plot_list[[42]] | plot_list[[41]]) /
  (plot_list[[32]] | plot_list[[33]] | plot_list[[35]] | plot_list[[34]]) /
  plot_layout(guides = "collect") +
  plot_annotation(title = "Clinical Chemistry")
dev.off()

tiff("Absolute organ weights.tiff", units="in", width=8, height=8, res=200)
(plot_list[[20]] | plot_list[[21]]) /
  (plot_list[[23]]  | plot_list[[25]]) /
  (plot_list[[27]]  | plot_list[[29]]) /
  #(plot_list[[25]] | plot_list[[27]]) /
  plot_layout(guides = "collect") +
  plot_annotation(title = "Absolute Organ Weights (grams)")
dev.off()

tiff("Relative organ weights.tiff", units="in", width=8, height=8, res=200)
(plot_list[[20]] | plot_list[[22]]) /
  (plot_list[[24]]  | plot_list[[26]]) /
  (plot_list[[28]]  | plot_list[[30]]) /
  #(plot_list[[26]] | plot_list[[28]]) /
  plot_layout(guides = "collect") +
  plot_annotation(title = "Relative Organ Weights (% of body weight)")
dev.off()


# library(patchwork)
#
# tiff("Relative organ weights.tiff", units="in", width=8, height=8, res=200)
# (plot_list[[13]]) /
#   (plot_list[[15]]  | plot_list[[17]]) /
#   plot_layout(guides = "collect") #+
#   #plot_annotation(title = "Relative Organ Weights (% of body weight)")
# dev.off()