library(tidyr) library(dplyr) library(multcomp) library(ggplot2) getwd() ## Set working directory setwd("C:/Users/blakebe/Documents/Harlie/HPLC data") ## Read in data file containing animal IDs, treatment groups, etc x<-read.csv("R format PND 5.5 pooled serum and urine.csv") str(x) names(x) levels(x$group) x$group<-factor(x$group, levels=c("Vehicle Control","0.1 mg/kg PFOA","1.0 mg/kg PFOA","0.2 mg/kg GenX","1.0 mg/kg GenX","2.0 mg/kg GenX")) summary.stats<-x%>% dplyr::group_by(group, matrix) %>% dplyr::summarise(mean.matrix = mean(ug.ml, na.rm = TRUE), sd.matrix = sd(ug.ml, na.rm = TRUE)) summary.stats #write.csv(summary.stats, "PND 5.5 pooled serum and urine summary stats.csv",row.names = F) summary.stats$ug.ml<-summary.stats$mean.matrix summary.stats$ug.ml.lo<-summary.stats$mean.matrix-summary.stats$sd.matrix summary.stats$ug.ml.hi<-summary.stats$mean.matrix+summary.stats$sd.matrix p1<-ggplot(summary.stats, aes(x=group, y=ug.ml))+ theme_bw()+ theme(legend.position="none", axis.text=element_text(size=12), axis.text.x=element_text(angle =-45, hjust=0), axis.title=element_text(size=14), plot.margin=unit(c(2,2,2,2),"cm"))+ geom_jitter(data=x, aes(x=group, y=ug.ml), position = position_jitter(width = 0.2))+ geom_crossbar(data=summary.stats, aes(ymin = ug.ml.lo, ymax = ug.ml.hi), width = 0.4)+ facet_wrap(matrix~., scales="free")+ ggtitle("PND 5.5 Pooled Pup Urine and Serum Dosimetry")+ ylab("Analyte concentration (ug/mL)\n")+ xlab("\nGroup") p1 tiff("PND 5.5 pooled serum urine dosimetry.tiff", units="in", width=9, height=7, res=300) # insert ggplot code p1 dev.off() ser<-subset(x, matrix=="pooled serum") ur<-subset(x, matrix=="pooled urine") summary(glht(aov(ng.ml~group, data=ser),linfct=mcp(group="Tukey"))) summary(glht(aov(ng.ml~group, data=ur),linfct=mcp(group="Tukey")))