################################################################
### AUC along Tolerance
################################################################
### Graphic Parameters
cols <- c("green3", "green3","green3","green3",
"red","red","red","red","red",
"cyan", "cyan","cyan","cyan","cyan",
"darkorchid4","darkorchid4","darkorchid4","darkorchid4","darkorchid4",
"orange","blue")
pchs <- 16
ltysDP <- c(2,3,4,1,
2,3,4,1,5,
2,3,4,1,5,
2,3,4,1,5,
1,1)
###
for(pp in pct){
source('00.setup.R')
pathFig <- sprintf("fig/AUC")
Arguments$getWritablePath(pathFig)
pathname = sprintf("%s/%s,PartialAUC,2dvs1d.pdf", pathFig, simName)
pdf(pathname, width = 10, height=10)
par(cex = 1.5, mar = c(4, 4, 2, 1)+0.1, mgp = c(2.5, 1, 0))
plot(NA, NA, xlim = c(0, max(tols)), ylim = c(0, 1), xlab = "Tolerance", ylab = "Partial AUC", cex.axis= 1.2, cex.lab = 1.4)
sapply(methTags, function(methTag){
AucPath <- "aucData"
fpath <- file.path(AucPath, simName)
fpath <- Arguments$getWritablePath(fpath)
filename <- sprintf("%s,B=%s,%s,aucData,relax=%s.xdr", simNameNF, B, methTag, relax)
pathname <- file.path(fpath, filename)
if(file.exists(pathname)){
auc <- loadObject(pathname)
mm <- which(methTags==methTag)
xx <- tols
lines(xx, auc[, "meanAUC"], col = cols[mm], lty=ltysDP[mm])
mom <- auc[, "masOmenoAUC"]
segments(xx, auc[, "meanAUC"]-mom, xx, auc[, "meanAUC"]+mom, col=cols[mm], lwd=1.8)
points(xx, auc[, "meanAUC"]-mom, pch="-", col=cols[mm])
points(xx, auc[, "meanAUC"]+mom, pch="-", col=cols[mm])
}
})
dev.off()
}
################################################################
### AUC along Contamination
################################################################
for(tol in tols){
print("AUC by contamination")
ss <- sprintf("ROC,n=%s,K=%s,regSize=%s,minL=%s", len, K, regSize, minL)
pathFig <- sprintf("fig/AUC")
Arguments$getWritablePath(pathFig)
pathname <- sprintf("%s/%s,tol=%s,PartialAUC,ContaminationInfluence.pdf", pathFig, ss, tol)
pdf(pathname, width = 10, height=10)
par(cex = 1.5, mar = c(4, 4, 2, 1)+0.1, mgp = c(2.5, 1, 0))
plot(NA, NA, xlim = c(50, 100), ylim = c(0, 1), xlab = "Tumour purity", ylab = "Partial AUC", cex.axis= 1.2, cex.lab = 1.4)
aucMeth <- sapply(methTags, function(methTag){
aucContamination <- NULL
aucContaminationMom <- NULL
for(pp in pct){
print(pp)
## source("R/00.setup.R")
simTag <- sprintf("ROC,n=%s,K=%s,regSize=%s,minL=%s,pct=%s", len, K, regSize, minL, pp)
simName <- sprintf("%s,%s", dataSet, simTag)
AucPath <- "aucData"
fpath <- file.path(AucPath, simName)
fpath <- Arguments$getWritablePath(fpath)
filename <- sprintf("%s,B=%s,%s,aucData,relax=%s.xdr", simName, B, methTag, relax)
pathname <- file.path(fpath, filename)
print(file.exists(pathname))
if(file.exists(pathname)){
auc <- loadObject(pathname)
indtol <- which(tols==tol)
aucContamination <- c(aucContamination, auc[indtol, "meanAUC"])
print(aucContamination)
aucContaminationMom <- c(aucContaminationMom, auc[indtol, "masOmenoAUC"])
}
}
if(!is.null(aucContamination)){
mm <- which(methTags==methTag)
xx <- as.numeric(pct)
print(methTag)
print(aucContamination)
lines(xx, aucContamination, col = cols[mm], lty=ltysDP[mm])
mom <- aucContaminationMom
segments(xx, aucContamination-mom, xx, aucContamination+mom , col=cols[mm], lwd=1.8)
points(xx, aucContamination-mom, pch="-", col=cols[mm])
points(xx, aucContamination+mom, pch="-", col=cols[mm])
return(aucContamination)
}
})
dev.off()
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.