plotTreeMap: Plot Phylogenies for samples

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

Plot Phylogenies for samples

Description

This function plots phylogenetic trees for samples.

Usage

plotTreeMap(para, valueID = "valueNorm", log = TRUE, rmQC = TRUE,
  nc = 8, treeType = "fan", width = 8, ...)

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
nc	The number of clusters
treeType	A character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial" or any unambiguous abbreviation of these.
width	The width and height of the graphics region in inches. The default values are 8.
...	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)
plotTreeMap(para,valueID="value")

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