metaX (version 1.4.0)

plotHeatMap: Plot heatmap

Description

This function plots heatmap.

Usage

plotHeatMap(para, valueID = "valueNorm", log = TRUE, rmQC = TRUE, zero2na = FALSE, colors = "none", width = 12, height = 8, saveRds = TRUE, ...)

Arguments

para

A metaXpara object

valueID

The name of the column that used for plot

log

A logical indicating whether to log the data

rmQC

A logical indicating whether to remove the QC samples

zero2na

A logical indicating whether to convert the value

colors

Color for heatmap

width

The width of the graphics region in inches. The default values are 12.

height

The height of the graphics region in inches. The default values are 8.

saveRds

Boolean, setting the argument to TRUE to save some objects to disk for debug. Only useful for developer. Default is TRUE.

...

Additional parameter

Value

none

Examples

library(faahKO)
xset <- group(faahko)
xset <- retcor(xset)
xset <- group(xset)
xset <- fillPeaks(xset)
peaksData <- as.data.frame(groupval(xset,"medret",value="into"))
peaksData$name <- row.names(peaksData)
para <- new("metaXpara")
rawPeaks(para) <- peaksData
sampleListFile(para) <- system.file("extdata/faahKO_sampleList.txt", 
    package = "metaX")
para <- reSetPeaksData(para)
para <- missingValueImpute(para)
plotHeatMap(para,valueID="value",width=6)