library(ggplot2)
library(viridis)
library(viridisLite)
library(tidyverse)

## Check working directory
getwd()

## Set working directory 
setwd("C:/Users/bblake/OneDrive - Environmental Protection Agency (EPA)/Profile/Documents/NTP TGMX/TGMX new/CSV")

## Read in data
x<-read.csv("Significant NES hallmark pathway maternal fetal liver.csv", header=T)

## Check data structure
str(x)

x$tissue<-as.factor(as.character(x$tissue))
x$dose<-as.factor(as.character(x$dose))
x$pathway<-as.factor(as.character(x$pathway))

x$tissue<-factor(x$tissue, levels=c("Maternal liver","Fetal liver"))
x$dose<-factor(x$dose, levels=c("1 mg/kg PFOA","5 mg/kg PFOA","2 mg/kg GenX","10 mg/kg GenX"))


x$pathway <- reorder(x$pathway, x$n.sig.all)

x$significance <- 1/x$p


p<-ggplot(x, aes(x=dose, 
             y=pathway, 
             colour=p, 
             size=NES)) +
  theme_bw()+
  geom_point() +
  facet_grid(~tissue)+
  scale_colour_viridis(direction=-1, begin = 0.05,end = 0.95,option="D")
  #labs(x="Group", y="Pathway", colour="NES", size="p value")+
  #scale_size(trans = 'reverse')
p



p<-ggplot(x, aes(x=pathway, 
                 y=NES, 
                 color=NES,
                 size=p)) +
  theme_bw()+
  geom_point() +
  facet_grid(tissue~dose)+
  coord_flip()+
  geom_hline(yintercept=0, color="gray", linetype="dashed")+
  scale_colour_viridis(direction=1, begin = 0.05,end = 0.95,option="D")+
  labs(y="Normalized Enrichment Score", colour="NES", size="p value")+
  scale_size(trans="reverse")
p

tiff("Hallmark Pathway NES.tiff", units="in", width=7.75, height=7.5, res=300)
x$n.sig.all<-as.factor(as.numeric(x$n.sig.all))
p<-ggplot(x, aes(x=pathway, 
                 y=NES, 
                 color=n.sig.all,
                 size=log(p))) +
  theme_bw()+
  geom_point() +
  facet_grid(tissue~dose)+
  coord_flip()+
  geom_hline(yintercept=0, color="gray", linetype="dashed")+
  scale_colour_viridis(direction=1, begin = 0 ,end = 0.94, option="D", discrete=TRUE)+
  labs(y="Normalized Enrichment Score", x="Hallmark Pathway", size="log10(p value)")+
  scale_size(trans="reverse")
p
dev.off()