plotHeatMap: Plot heatmap

Description Usage Arguments Value Author(s) Examples

Description

This function plots heatmap.

Usage

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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 <=0 to NA

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

Author(s)

Bo Wen wenbo@genomics.cn

Examples

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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)

metaX documentation built on Oct. 5, 2016, 4:41 a.m.

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