# Author: ahrnee-adm
###############################################################################
### INIT
if(!grepl("SafeQuant\\.Rcheck",getwd())){
setwd(dirname(sys.frame(1)$ofile))
}
source("initTestSession.R")
### INIT END
pValueThrs = 0.01
log2RatioThrs=0.001
thrsLineCol = "lightgrey"
thrsLineLty = 2
intensity = apply(getSignalPerCondition(sqa$eset)[,1:2],1,max, na.rm=T)
ggDf = data.frame(ratio = sqa$ratio[,1], pValue = sqa$pValue[,1]
, geneName = fData(sqa$eset)$proteinName
, ac=NA
, intensity = intensity
, description=fData(sqa$eset)$proteinDescription
, naHighLightSel= c(rep(T,300),rep(F,600))
, naCat = factor(c(rep("ctrl",100), rep("case",100), rep("both",100), rep("none",600)), levels = c("ctrl","case","both","none"))
)
#ggDf[ggDf$geneName == "REV_prot158",]
tmpFile <- paste(tempdir(),"/tmp_ggplot.pdf",collapse="",sep="")
pdf(tmpFile)
plot(ggVolcanoPlot(data=ggDf,pValueThrs=pValueThrs,log2RatioThrs=log2RatioThrs,thrsLineCol = "lightgrey",thrsLineLty = 2, title="test title"))
dev.off()
cat("CREATED FILE", tmpFile, "\n")
#plotAllGGVolcanoes(sqa)
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