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filename_top <- '../../data/03_ShawnJe/Je201608_MouseArray/Je201608_MouseArray_v3.top.txt';
tbl <- read.table(filename_top, header=T,row.names='ProbeID' )
filename_go <- '../../data/03_ShawnJe/Je201608_MouseArray/Je201608_MouseArray_v3.serotonineGO_top.txt';
tbl_go <- read.table(filename_go, header=T,row.names='ProbeID' )
filename_r <- '../../data/03_ShawnJe/Je201608_MouseArray/Je201608_MouseArray_v3.HTR_top.txt';
tbl_r <- read.table(filename_r, header=T,row.names='ProbeID' )
filename_t <- '../../data/03_ShawnJe/Je201608_MouseArray/Je201608_MouseArray_v3.transporter_top.txt';
tbl_t <- read.table(filename_t, header=T,row.names='ProbeID' )
filename_s <- '../../data/03_ShawnJe/Je201608_MouseArray/Je201608_MouseArray_v3.synthase_top.txt';
tbl_s <- read.table(filename_s, header=T,row.names='ProbeID' )
pdf("plot.pdf")
library(repr)
options(repr.plot.width=8, repr.plot.height=6)
par(mar = c(8,5,2,2) + 0.1)
smoothScatter(tbl$AveExpr, tbl$logFC, xlab="Average Expression", ylab="log2FC", ylim=range(-2,2))
points(tbl_go$AveExpr, tbl_go$logFC, pch=15, col='blue')
points(tbl_r$AveExpr, tbl_r$logFC, pch=16, col='magenta')
points(tbl_t$AveExpr, tbl_t$logFC, pch=17, col='orange')
points(tbl_s$AveExpr, tbl_s$logFC, pch=18, col='red')
legend("topright",legend=c("Receptors", "Transporters","Synthase","GO term related"), col=c("magenta", "orange", "red", "blue"), pch=c(16,17,18,15))
grid()
dev.off()
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