plotLoading: Plot figures for PCA/PLS-DA loadings

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

Plot figures for PCA/PLS-DA loadings

Description

Plot figure for PCA/PLS-DA loadings

Usage

plotLoading(object, out.tol = 0.9, show.outlier = FALSE, label = 0,
  fig = "loading.png")

Arguments

object	object of pcaRes or PLS-DA
out.tol	control the points to show labels
show.outlier	Logical. The points will be colour-coded when the value is set as TRUE. Default is FALSE
label	0=>only show part of the labels, 1=>show all the labels, 3=none labels

Value

none

Author(s)

Bo Wen [e-mail]

See Also

plotPCA

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")
res <- metaX::plotPCA(para,valueID="value",scale="uv",center=TRUE)
plotLoading(res$pca,fig="loading.png")

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