plotHeatMap: Plot heatmap

In wenbostar/metaX: A flexible and comprehensive software for processing omics data.

Plot heatmap

Description

This function plots heatmap.

Usage

plotHeatMap(para, valueID = "valueNorm", log = TRUE, rmQC = TRUE,
  zero2na = FALSE, colors = "none", anno = NULL, width = 12,
  height = 8, saveRds = TRUE, show_rownames = FALSE,
  show_colnames = FALSE, classCol = NULL, seriation = FALSE, ...)

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
anno	A file or a data frame including sample annotation data.
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 [e-mail]

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)

wenbostar/metaX documentation built on July 4, 2023, 7:50 p.m.