Nothing
PairsFun <-
function(inputframe,DensMatrixTemplate = NULL,pdfshow = F,pdfname = "pairsfun.pdf",filterMQQC = T,makepdf = T,mainvec = NULL,SelectMatrix = NULL){
panel.cor <- function(x, y, digits = 2, prefix = "", cex.cor, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
sel <- is.na(x)|is.na(y)|is.infinite(x)|is.infinite(y)
error <- class(try(ct <- cor.test(x[!sel], y[!sel]),silent = T))
if(error != "try-error"){
try(r <- (ct$estimate))
txt <- format(c(r, 0.123456789), digits = digits)[1]
txt <- paste0(prefix, txt)
if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
cexfinal <- cex.cor * abs(r)
if(cexfinal < 0.4){cexfinal <- 0.4}
text(0.5, 0.5, txt, cex = cexfinal,pos = 3)
text(0.5, 0.45, paste("n =",length(sel[!sel])), cex = 1.2,pos = 1,col = "darkgrey")
text(0.5, 0.2, paste("p =",signif(ct$p.value)), cex = 1.2,col = "darkgrey")
}
}
if(makepdf){
pdf(pdfname,width = 15,height = 15)
}
if(length(DensMatrixTemplate) > 0){
cselect <- sapply(DensMatrixTemplate[,1],function(x){grep(x,colnames(inputframe))})
nam <- DensMatrixTemplate[,2]
d <- inputframe[,cselect]
}else{
d <- inputframe
}
if(filterMQQC){
dl<- sapply(c("Intensity.50.","mass.error.uncal.50.","msmsQuantile.50.","ret.peak.shape.50."),function(x){grep(x,colnames(d))})
}else{
dl <- 1:dim(d)[2]
}
d[,dl] <- log10(d[,dl])
d <- apply(d,2,function(x){
xn <- rank(x)
xn[is.na(x)] <- NA
return(xn)
})
mnames <- ""
try(mnames <- strsplitslot(inputframe$Name,1,"_"))
if(length(mnames)==0){
mnames = rep(1,dim(inputframe)[1])
}
for(i in unique(mnames)){
ds <- d[mnames == i,]
dsNArem <- apply(ds,2,function(x){all(is.na(x))})
ds <- ds[,!dsNArem]
if(length(mainvec) !=0){
i <- mainvec
}
lp <- function(x,y,rcol = c("black","blue","green","yellow","orange","red"),...){
#cols = densCols(x,y,colramp = colorRampPalette("#14780960","black"))
x <- x
y <- y
if(length(x[!is.na(x)]) > 1){
try(points(x,y,col = densCols(x,y,colramp = colorRampPalette(rcol)),cex = 0.8,...),silent = T)
try(MFU <- medwin(x,y,win = 20),silent = T)
try(points(MFU$x,MFU$y,col = "red",type = "l"),silent = T)
try( abline(0,1,col = "grey20",lty = "dashed",lwd = 2),silent = T)
}else{
try(points(1,type = "n",...),silent = T)
legend("top",legend = "not enough\ndatapoints",x.intersp = 0,bty = "n")
}
}
if(length(DensMatrixTemplate) > 0){
ren <- paste(DensMatrixTemplate[,4],DensMatrixTemplate[,2],sep = ":\nranks\n")[match(colnames(ds),DensMatrixTemplate[,1])]
colnames(ds)[!is.na(ren)] <- ren[!is.na(ren)]
}
ds <<- ds
apply(ds,2,function(x){all(is.na(x))})
try( pairs(ds,upper.panel = panel.cor,lower.panel = lp,pch = 20,main = i),silent = T)
}
if(makepdf){
dev.off()
}
if(pdfshow){
system(paste("open",pdfname))
}
}
# try(PairsFun(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = T),silent = T)
# try(PairsFun(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = T),silent = T)
# try(PairsFun(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = T))
# graphics.off()
# PairsFun(subs,filterMQQC = F,makepdf = F)
# try(PairsFun(tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = T))
# PairsFun(SPD,filterMQQC = F,makepdf = F)
# PairsFun(hnm,filterMQQC = F,makepdf = F,mainvec = "Change")
# PairsFun(lfqplot)
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