#Pie charts based on GO Slim for biological processes enriched in individual oysters in the ambient control group for ALR proteomics manuscript
setwd('/Users/emmatimminsschiffman/Documents/Dissertation/proteomics/DB post-genome/DAVID')

goslim<-read.csv('enriched GO Slim ambient OT.csv', header=T)

#'burlywood4', 'cadetblue', 'blueviolet', 'palegreen3', 'lightcoral', 'bisque2', 'black', 'aquamarine3', 'darkgoldenrod2', 'plum3', 'darkred', 'deeppink3'
#colors correspond in order to GO Slim terms: cell adhesion, cell cycle & proliferation, cell organization & biogenesis, cell-cell signaling, death, developmental processes, DNA metabolism, protein metabolism, RNA metabolism, signal transduction, stress response, transport


pie(goslim$number.221[1:6], col=c('cadetblue','lightcoral', 'bisque2', 'darkgoldenrod2', 'darkred', 'deeppink3'), labels=rep(' ', 6))

pie(goslim$number.224[1:6], col=c('cadetblue','blueviolet', 'bisque2', 'darkgoldenrod2', 'darkred', 'deeppink3'), labels=rep(' ', 6))

pie(goslim$number.227[1:8], col=c('cadetblue','blueviolet', 'lightcoral', 'bisque2', 'darkgoldenrod2','plum3', 'darkred', 'deeppink3'), labels=rep(' ', 8))

pie(goslim$number.230[1:6], col=c('burlywood4', 'cadetblue','lightcoral', 'bisque2', 'darkgoldenrod2', 'darkred'), labels=rep(' ', 6))

#Pie chart for entire orbitrap proteome, SPID cutoff of 1e-10, spectral count cut-off of at least 4 spectra
setwd('/Users/emmatimminsschiffman/Documents/Dissertation/proteomics/DB post-genome')

prot2<-read.csv('ambient proteome 2 pie.csv', header=F)

pie(prot2$V2, col=c('burlywood4', 'cadetblue', 'blueviolet', 'palegreen3', 'lightcoral', 'bisque2', 'black', 'aquamarine3', 'darkgoldenrod2', 'plum3', 'darkred', 'deeppink3'), labels=rep(' ', 12))


#Pie chart for enrichment of proteome ambient 2 OT vs. entire proteome
protenrich<-c(4,8,73,36,32,12,2,7,11)
pie(protenrich, col=c('burlywood4', 'cadetblue', 'blueviolet', 'bisque2','aquamarine3', 'darkgoldenrod2', 'plum3', 'darkred', 'deeppink3'), labels=rep(' ', 9))