metaX (version 1.4.0)

plotTreeMap: 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

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")