metaX (version 1.4.0)

plotPCA: Plot PCA figure

Description

Plot PCA figure

Usage

plotPCA(para, pcaMethod = "svdImpute", valueID = "valueNorm", label = "order", rmQC = TRUE, batch = FALSE, scale = "none", center = FALSE, saveRds = TRUE, ...)

Arguments

para

A metaXpara object

pcaMethod

See pca in pcaMethods

valueID

The name of the column which will be used

label

The label used for plot PCA figure, default is "order"

rmQC

A logical indicates whether remove QC data

batch

A logical indicates whether output batch information

scale

Scaling, see pca in pcaMethods

center

Centering, see pca in pcaMethods

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

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)
para <- transformation(para,valueID = "value")
metaX::plotPCA(para,valueID="value",scale="uv",center=TRUE)