plotCorHeatmap: Plot correlation heatmap

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

Plot correlation heatmap

Description

This function plots correlation heatmap.

Usage

plotCorHeatmap(para, valueID = "value", samples = NA,
  label = "order", width = 6, cor.method = "spearman",
  sortBy = "class", colorRange = NULL, height = 6, anno = FALSE,
  cluster = FALSE, shownames = FALSE, classCol = NULL, ...)

Arguments

para	A metaXpara object
valueID	The name of the column that used for plot
samples	Samples used for plot
label	Label to show in figure
width	The width of the graphics region in inches. The default values are 6.
cor.method	Method used for correlation
sortBy	Sort the sample name according the this value, default is "class". This is valid when cluster is FALSE. Valid value: class, order, batch. This parameter is useful to sort the sample name according to batch name when users want to check batch effect.
colorRange	The color range of heatmap.
height	The height of the graphics region in inches. The default values are 6.
anno	A logical value indicates whether to plot heatmap with annotating class information
cluster	A logical value indicates whether to do the cluster when anno is TRUE
shownames	A logical indicates whether show names when plot
...	Additional parameter

Value

The fig name

Author(s)

Bo Wen [e-mail]

Examples

para <- new("metaXpara")
pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
sampleListFile(para) <- sfile
para <- reSetPeaksData(para)
para <- missingValueImpute(para)
plotCorHeatmap(para,valueID="value",samples=NULL,width=6,anno=TRUE)

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