plotPCA: Plot PCA figure

In metaX: An R package for metabolomic data analysis

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

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

metaX documentation built on Oct. 5, 2016, 4:41 a.m.