Nothing
setMethodS3("plotDecompAroma", "ProbeLevelModel",
plotDecompAroma<-function(plm,id="7952953",col="black",lwd=1,vlines=NULL) {
library("aroma.affymetrix")
ces <- getChipEffectSet(plm)
rs <- getResidualSet(plm)
ds <- getDataSet(plm)
paf <- getProbeAffinities(plm)
cdf <- getCdf(plm)
if (is.integer(id))
unit <- id
else
unit <- which( getUnitNames(cdf)== id)
if (length(unit) != 1)
stop("can only have 1 unit plotted.")
pe <- log2(readUnits(paf,units=unit)[[1]][[1]]$phi)
r <- log2(readUnits(rs,units=unit)[[1]][[1]]$eps)
d <- log2(readUnits(ds,units=unit)[[1]][[1]]$intensities)
ch <- log2(readUnits(ces,units=unit)[[1]][[1]]$intensities)
if(length(col)==ncol(r)) {
o<-order(col,decreasing=TRUE)
col<-col[o]
lwd<-lwd[o]
} else {
o<-1:ncol(r)
}
par(mfrow=c(2,2))
xl<-"Probe Index"
matplot(d,xlab="",ylab="",main="",lty=1,type="l",col=col,lwd=lwd)
abline(v=vlines,lty=3)
plot(pe,type="h",main="",xlab="",ylab="")
matplot(ch,xlab="",ylab="",main="",lty=1,type="l",col=col,lwd=lwd)
abline(v=vlines,lty=3)
matplot(r[,o],xlab=xl,ylab="",main="",lty=1,type="l",col=col,lwd=lwd)
abline(v=vlines,lty=3)
invisible(list(data=d,residuals=r,probeeffects=pe,chipeffects=ch,col=col,lwd=lwd))
}) # plotDecompAroma
.plotDecomp <- function(obj,id="7952953",col="black",lwd=1,vlines=NULL) {
par(mfrow=c(2,2))
pe<-obj@probe.coefs[[id]]
pe<-c(pe,-sum(pe))
r<-obj@residuals$PM.resid
r<-r[which(rownames(r)==id),]
ce<-obj@chip.coefs[id,]
y<-r+outer(rep(1,nrow(r)),ce)+outer(pe,rep(1,ncol(r)))
pay<-r+outer(rep(1,nrow(r)),ce)
if(length(col)==ncol(r)) {
o<-order(col,decreasing=TRUE)
col<-col[o]
lwd<-lwd[o]
} else {
o<-1:ncol(r)
}
par(mfrow=c(2,2))
xl<-"Probe Index"
matplot(y[,o],xlab="",ylab="",main=paste("BG Corrected, Normalized data","--",id,sep=""),lty=1,type="l",col=col,lwd=lwd)
abline(v=vlines,lty=3)
plot(pe,type="h",main="Probe Effects",xlab="",ylab="")
matplot(pay[,o],xlab=xl,ylab="",main="Probe-adjusted Expression",lty=1,type="l",col=col,lwd=lwd)
abline(v=vlines,lty=3)
matplot(r[,o],xlab=xl,ylab="",main="Residuals",lty=1,type="l",col=col,lwd=lwd)
abline(v=vlines,lty=3)
invisible(list(data=y,residuals=r,probeadjusted=pay,probeeffects=pe,col=col,lwd=lwd))
}
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