## CD-1 PFOA/GenX gestational exposure and latent health outcomes study ## Implant and percent viable data ## Number of implantations, percent viable(#live on PND0.5/#implants) ## File: "ImplantsQC" ## HAC 01/22/2020 (w/ QC data) ## Load packages (needs to be done every time R is opened, but not for each individual file) library(dplyr) library(lme4) library(ggplot2) library(multcomp) library(tidyverse) # 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 (import dataset -> From Text (readr) -> choose file (don't change any parameters)->run every line after 18) x<- read_csv("~/Desktop/GenX:PFOA Study/GenX PFOA Mouse Study/QC Data Files/csv for R/QCImplants.csv") x$Dam.ID<-as.factor(x$Dam.ID) x$Group<-as.factor(x$Group) str(x) implants<-x names(implants) implants.summary.stats<-implants%>% group_by(Group)%>% summarise( implants.mean=mean(Implants, na.rm=T), implants.sd=sd(Implants, na.rm=T), viable.mean=mean(percentviable, na.rm=T), viable.sd=sd(percentviable, na.rm=T), ) implants.summary.stats write.csv(implants, "Implants and percent viable.csv",row.names = F) ### Statistical Analyses ## Implants summary(glht(aov(Implants~Group,data=implants), linfct=mcp(Group="Dunnett"))) ## No differences ##percent viable summary(glht(aov(percentviable~Group,data=implants), linfct=mcp(Group="Dunnett"))) ## No differences implantplot<-ggplot(implants.summary.stats, aes(x=group, y=implants.mean, group=Group))+ theme_bw()+ theme(axis.text=element_text(size=12))+ theme(axis.text.x = element_text(angle = 45, hjust = 1))+ geom_jitter(data=implants, aes(x=Group, y=Implants, color=Group), size=1.9, alpha=0.5,position=position_jitter(width=0.2))+ geom_errorbar(data=implants.summary.stats, mapping=aes(x=Group, ymin=implants.mean-implants.sd, ymax=implants.mean+implants.sd, color=Group), width=0.2, size=1) + geom_point(data=implants.summary.stats, mapping=aes(x=Group, y=implants.mean, color=Group), size=4, shape=3) + ggtitle("Implants (mean +/- SD)\n")+ xlab("\n Group")+ ylab("# Implants") implantplot viableplot<-ggplot(implants.summary.stats, aes(x=group, y=viable.mean, group=Group))+ theme_bw()+ theme(axis.text=element_text(size=12))+ theme(axis.text.x = element_text(angle = 45, hjust = 1))+ geom_jitter(data=implants, aes(x=Group, y=percentviable, color=Group), size=1.9, alpha=0.5,position=position_jitter(width=0.2))+ geom_errorbar(data=implants.summary.stats, mapping=aes(x=Group, ymin=viable.mean-viable.sd, ymax=viable.mean+viable.sd, color=Group), width=0.2, size=1) + geom_point(data=implants.summary.stats, mapping=aes(x=Group, y=viable.mean, color=Group), size=4, shape=3) + ggtitle("Percent Viable (mean +/- SD)\n")+ xlab("\n Group")+ ylab("% Viable") viableplot