## CD-1 PFOA/GenX gestational exposure and latent health outcomes study
## Week 17 Bruker
## Fat:lean and percent fat
## HAC 01/26/2020 (w/ QC data)

## Load packages (needs to be done every time R is opened)
library(dplyr)
library(lme4)
library(ggplot2)
library(multcomp)
library(tidyverse)
library(viridis)
# Set your working directory (replace this example with your file folder destination)
setwd("/Users/harliecope/Desktop/GenX:PFOA Study/GenX PFOA Mouse Study/GenXPFOA Study")

# Read in your files
x<- read_csv("~/Desktop/GenX:PFOA Study/GenX PFOA Mouse Study/QC Data Files/csv for R/Week17BrukerBarGraphGrams.csv")
x$Group<-as.factor(x$Group)
x$Group<-factor(c("Control", "0.2 mg/kg GenX", "1.0 mg/kg GenX", "2.0 mg/kg GenX", "0.1 mg/kg PFOA", "1.0 mg/kg PFOA"), 
                levels=c("Control", "0.2 mg/kg GenX", "1.0 mg/kg GenX", "2.0 mg/kg GenX", "0.1 mg/kg PFOA", "1.0 mg/kg PFOA"))


str(x)

w17bruker<-x


### Statistical Analyses

## Statistical analysis
## Males

w17m<-subset(w17bruker, Sex=="Male")
w17f<-subset(w17bruker, Sex=="Female")

w17mhf<-subset(w17m, Diet=="HFD")
w17mlf<-subset(w17m, Diet=="LFD")
w17fhf<-subset(w17f, Diet=="HFD")
w17flf<-subset(w17f, Diet=="LFD")


##MHFD
MHFDplot<-ggplot(w17mhf, aes(fill=Compartment, y=Grams, x=Group)) + 
  geom_bar(position="stack", stat="identity") +
  scale_fill_viridis(discrete=TRUE, begin = 0.3, end = 0.8, option="magma")+
  theme_bw()+
  theme(axis.text=element_text(size=12),
        axis.text.x = element_text(angle = 45, hjust = 1))
print(MHFDplot + ggtitle("Male HFD"))

##MLFD
MLFDplot<-ggplot(w17mlf, aes(fill=Compartment, y=Grams, x=Group)) + 
  geom_bar(position="stack", stat="identity") +
  scale_fill_viridis(discrete=TRUE, begin = 0.3, end = 0.8, option="magma")+
  theme_bw()+
  theme(axis.text=element_text(size=12),
        axis.text.x = element_text(angle = 45, hjust = 1))
print(MLFDplot + ggtitle("Male LFD"))

##FHFD
FHFDplot<-ggplot(w17fhf, aes(fill=Compartment, y=Grams, x=Group)) + 
  geom_bar(position="stack", stat="identity")+
  scale_fill_viridis(discrete=TRUE, begin = 0.3, end = 0.8, option="magma")+
  theme_bw()+
  theme(axis.text=element_text(size=12),
        axis.text.x = element_text(angle = 45, hjust = 1))
print(FHFDplot + ggtitle("Female HFD"))

##FLFD
FLFDplot<-ggplot(w17flf, aes(fill=Compartment, y=Grams, x=Group)) + 
  geom_bar(position="stack", stat="identity")+
  scale_fill_viridis(discrete=TRUE, begin = 0.3, end = 0.8, option="magma")+
  theme_bw()+
  theme(axis.text=element_text(size=12),
        axis.text.x = element_text(angle = 45, hjust = 1))
print(FLFDplot + ggtitle("Female LFD"))