Nothing
# setMethod("boxplot",
# signature(x = "beadLevelData"),
# function (x, transFun=logGreenChannelTransform,...)
# {
#
# arraynms = sectionNames(x)
# narrays = length(arraynms)
#
# inten <- unlist(lapply(1:narrays, function(i) transFun(x, array=i)))
# section <- NULL
#
# for(i in 1:narrays){
#
# section <- c(section, rep(sectionNames(x)[i], numBeads(x)[i]))
# }
#
# df <- data.frame(Value = inten, Section = section)
#
# p <- ggplot(df, aes(x = factor(Section), y = Value, fill=factor(Section))) + geom_boxplot(outlier.shape=NA)
# p
# }
# )
setGeneric("boxplot", function(x,...) standardGeneric("boxplot"))
setMethod("boxplot",
signature(x = "beadLevelData"),
function (x, transFun=logGreenChannelTransform,...)
{
tmp = list()
arraynms = sectionNames(x)
narrays = length(arraynms)
for(i in 1:narrays){
tmp[[arraynms[i]]] = transFun(x, array=i)
}
boxplot(tmp,...)
}
)
setMethod("boxplot",
signature(x = "ExpressionSetIllumina"),
function (x, what="exprs",probeFactor = NULL, SampleGroup=NULL, facet = NULL,plot=FALSE,...)
{
addedSampleGroup <- addedProbeFactor <- FALSE
data <- melt(assayDataElement(x, what))
if(!is.null(SampleGroup)){
if(SampleGroup %in% colnames(pData(x))){
data <- data.frame(data, SampleGroup = pData(x)[match(data[,"Var2"], rownames(pData(x))),SampleGroup])
addedSampleFactor <- TRUE
}
else message("Could not find a phenoData column called " , SampleGroup)
}
if(!is.null(probeFactor)){
if(probeFactor %in% colnames(fData(x))){
data <- data.frame(data, probeFactor = fData(x)[match(data[,"Var1"], rownames(fData(x))),probeFactor])
addedProbeFactor <- TRUE
}
else message("Could not find a featureData column called " , probeFactor)
}
##Traditional boxplot of all probes on every array vs array.
if(!(addedSampleGroup) & !(addedProbeFactor)){
p <- ggplot(data, aes(x = factor(Var2), y = value)) + geom_boxplot(outlier.shape=NA,fill="steelblue")
}
##Change x axis to vary with the new probe factor
else if(addedProbeFactor){
p <- ggplot(data, aes(x = factor(probeFactor), y = value, fill=factor(probeFactor))) + geom_boxplot(outlier.shape=NA) + scale_fill_discrete(name=probeFactor)
if(addedSampleGroup){
p <- p + facet_wrap(~SampleGroup)
}
else p <- p + facet_wrap(~Var2)
}
##change x axis to vary with new sample factor
else if(addedSampleGroup){
p <- ggplot(data, aes(x = factor(SampleGroup), y = value, fill=factor(SampleGroup))) + geom_boxplot(outlier.shape=NA) + scale_fill_discrete(name=SampleGroup)
}
p + theme(axis.title.x = element_blank(),axis.text.x = element_text(angle=90),axis.title.y=element_text(angle=0)) + ylab(what)
}
)
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