plotPCA: Performa PCA analysis and plot PCA figure

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

Performa PCA analysis and plot PCA figure

Description

Performa PCA analysis and plot PCA figure

Usage

plotPCA(para, pcaMethod = "svdImpute", valueID = "valueNorm",
  label = "order", pointLabel = NULL, pointSize = 1.4,
  labelSize = 4, rmQC = TRUE, batch = FALSE, showCircle = TRUE,
  showClass = TRUE, scale = "none", center = FALSE, saveRds = TRUE,
  legendRowBatch = NULL, legendRowClass = NULL,
  legendPosition = "top", classColor = NULL, pdfWidth = 4.38,
  pdfHeight = 3.7, pngWidth = 4, pngHeight = 4.2, res = 120,
  plot3d = FALSE, reverse = FALSE, ...)

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". This value can be "order" or "sample". If the value of this parameter is NA or NULL, then no label will be shown for each point.
pointLabel	The labels for each point, default is NULL. When users want to highlight some samples, this parameter is useful.
pointSize	The size of the point, default is 1.4
labelSize	The size of the label, default is 4
rmQC	A logical indicates whether remove QC data
batch	A logical indicates whether output batch information
showCircle	Whether or not to show circle for each class, default is TRUE.
showClass	Whether or not to show class information, default is TRUE. This parameter is useful when users want to check the batch effect.
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.
legendRowBatch	Specify the number of column of legend for batch. Default is NULL and use the default setting.
legendRowClass	Specify the number of column of legend for group. Default is NULL and use the default setting.
classColor	A data frame for color setting of class
pdfWidth	Width for PDF, default is 4.38
pdfHeight	Height for PDF, default is 3.7
pngWidth	Width for PNG, default is 4 inch
pngHeight	Height for PNG, default is 4.2 inch
res	resolution for PNG, default is 120
reverse	Default is FALSE. Change type between class and batch.
...	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)

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