## CD-1 PFOA/GenX gestational exposure and latent health outcomes study
## Week 18 Liver Pathology Severity Scores
## HAC 05/16/2020 (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(RVAideMemoire)

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/Week18Pathyn.csv")
x$ID <-as.factor(x$ID)
x$Group<-as.factor(x$Group)
str(x)

w18path<-x

highfat<-subset(w18path, Diet=="H")
lowfat<-subset(w18path, Diet=="L")

w18m<-subset(w18path, Sex=="M")
w18f<-subset(w18path, Sex=="F")

w18mhf<-subset(w18m, Diet=="H")
w18mlf<-subset(w18m, Diet=="L")
w18fhf<-subset(w18f, Diet=="H")
w18flf<-subset(w18f, Diet=="L")

##mixed cell infiltrate
fisher.test(table(w18mhf$Group,w18mhf$MCI)) ##not sig

fisher.test(table(w18mlf$Group,w18mlf$MCI)) ##not sig

fisher.test(table(w18fhf$Group,w18fhf$MCI)) ##not sig

fisher.test(table(w18flf$Group,w18flf$MCI)) ##not sig
##no differences

##hepatocyte single cell necrosis
fisher.test(table(w18mhf$Group,w18mhf$HSCN)) ##not sig

fisher.test(table(w18mlf$Group,w18mlf$HSCN)) ##not sig

fisher.test(table(w18fhf$Group,w18fhf$HSCN))
fisher.multcomp(table(w18fhf$Group,w18fhf$HSCN), p.method = "none")
pvalues<-c(1, 0.0128205, 0.2848297, 0.5459236, 0.0009228)
p.adjust(pvalues, method = "holm")
##adjusted values 1.0000000 0.0512820 0.8544891 1.0000000 0.0046140*

fisher.test(table(w18flf$Group,w18flf$HSCN)) ##not sig
##female high fat control vs 1.0 mg/kg PFOA 0.0046140

## fat micro
fisher.test(table(w18mhf$Group,w18mhf$FATmicro)) ##not sig

fisher.test(table(w18mlf$Group,w18mlf$FATmicro)) 
fisher.multcomp(table(w18mlf$Group,w18mlf$FATmicro), p.method = "none")
pvalues<-c(1, 0.205882, 0.004721, 0.082353, 0.205882)
p.adjust(pvalues, method = "holm")
##adjustedvalues 1.000000 0.617646 0.023605* 0.329412 0.617646

fisher.test(table(w18fhf$Group,w18fhf$FATmicro)) ##not sig

fisher.test(table(w18flf$Group,w18flf$FATmicro)) ##not sig
## increase in fat micro for GenX2.0 mg/kg males p=0.023605

##Fat macro
fisher.test(table(w18mhf$Group,w18mhf$FATmacro)) ##not sig

fisher.test(table(w18mlf$Group,w18mlf$FATmacro)) ##not sig

fisher.test(table(w18fhf$Group,w18fhf$FATmacro)) ##not sig

fisher.test(table(w18flf$Group,w18flf$FATmacro)) ##not sig
##no differences


##subset by diet no sex

##MCI
fisher.test(table(lowfat$Group,lowfat$MCI))

fisher.test(table(highfat$Group,highfat$MCI))
##no differences

##HSCN
fisher.test(table(lowfat$Group,lowfat$HSCN))

fisher.test(table(highfat$Group,highfat$HSCN))
fisher.multcomp(table(highfat$Group,highfat$HSCN), p.method = "none")
pvalues<-c(1, 0.0057246, 0.3430672, 1, 0.0006583)
p.adjust(pvalues, method="holm")
## adjusted pvalues 1.0000000 0.0228984* 1.0000000 1.0000000 0.0032915
## high fat control vs 1.0 mg/kg GenX p=0.0229, 1.0 mg/kg PFOA p=0.00329

##Fatmicro
fisher.test(table(lowfat$Group,lowfat$FATmicro))
fisher.multcomp(table(lowfat$Group,lowfat$FATmicro), p.method = "none")
pvalues<-c(0.045455, 0.015698, 0.003091, 0.019062, 0.046332)
p.adjust(pvalues, method="holm")
##adjusted p values 0.090910 0.062792 0.015455 0.062792 0.090910
##difference between control and 2.0 mg/kg GenX p=0.015455

fisher.test(table(highfat$Group,highfat$FATmicro)) ## not sig

##fat macro
fisher.test(table(lowfat$Group,lowfat$FATmacro))

fisher.test(table(highfat$Group,highfat$FATmacro))
##no differences