library("flowCore")
dataDir = "Desktop/work/citrus/data/syntheticData/example3/"
genBasePop = function(x){
pop1 = matrix(rnorm(nEvents*percents[1]*2),ncol=2)
pop2 = matrix(rnorm(nEvents*percents[2]*2,mean=3.5),ncol=2)
pop3 = cbind(rnorm(nEvents*percents[3],mean=3.5),rnorm(nEvents*percents[3]))
return(rbind(pop1,pop2,pop3))
}
nEvents = 10000
percents = c(0.6,.25,.15)
for (i in 1:10){
for (diseaseState in c("healthy","diseased")){
trueLabels = c(rep(1,nEvents*percents[1]),rep(2,nEvents*percents[2]),rep(3,nEvents*percents[3]))
fBase = rnorm(1,mean=1)
if (diseaseState=="diseased"){
fStim = fBase + abs(rnorm(1,sd=.5,mean=1))
} else {
fStim = fBase
}
print(paste(fBase,fStim))
f1Unstim = rnorm(nEvents,mean=2)
f1Stim1 = rnorm(nEvents,mean=2)
f2Unstim = rnorm(nEvents,mean=fBase)
f2Stim1 = rnorm(nEvents,mean=fBase)
f2Stim1[trueLabels==3]=rnorm(sum(trueLabels==3),mean=fStim)
if (diseaseState=="diseased"){
patientId = i+10;
} else {
patientId=i;
}
patientIdStim = paste("Patient",sprintf("%02.0f",patientId),"_",diseaseState,"_stim1.fcs",sep="")
patientIdUnstim = paste("Patient",sprintf("%02.0f",patientId),"_",diseaseState,"_unstim.fcs",sep="")
patientUnstimData = cbind(genBasePop(),f1Unstim,f2Unstim,trueLabels)
patientStimData = cbind(genBasePop(),f1Stim1,f2Stim1,trueLabels)
patientUnstimData = patientUnstimData[sample(1:nEvents),]
patientStimData = patientStimData[sample(1:nEvents),]
colnames(patientUnstimData) = c("LineageMarker1","LineageMarker2","FunctionalMarker1","FunctionalMarker2","trueLabel")
colnames(patientStimData) = c("LineageMarker1","LineageMarker2","FunctionalMarker1","FunctionalMarker2","trueLabel")
plot(density(patientUnstimData[patientUnstimData[,"trueLabel"]==2,3]))
lines(density(patientStimData[patientStimData[,"trueLabel"]==2,3]))
plot(density(patientUnstimData[patientUnstimData[,"trueLabel"]==3,3]))
lines(density(patientStimData[patientStimData[,"trueLabel"]==3,3]))
plot(density(patientUnstimData[patientUnstimData[,"trueLabel"]==2,4]))
lines(density(patientStimData[patientStimData[,"trueLabel"]==2,4]))
plot(density(patientUnstimData[patientUnstimData[,"trueLabel"]==3,4]))
lines(density(patientStimData[patientStimData[,"trueLabel"]==3,4]))
write.FCS(flowFrame(patientUnstimData),filename=file.path(dataDir,patientIdUnstim))
write.FCS(flowFrame(patientStimData),filename=file.path(dataDir,patientIdStim))
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.