plotPCA: A function for plotting PCA plots.
In mrbin: Metabolomics Data Analysis Functions

plotPCA

R Documentation

A function for plotting PCA plots.

Description

This function performs PCA, then plots PC1 and PC2.

Usage

plotPCA(
  mrbinResults,
  defineGroups = TRUE,
  loadings = FALSE,
  legendPosition = "bottomleft",
  annotate = TRUE,
  verbose = TRUE,
  xpd = NA
)

Arguments

`mrbinResults`	An mrbin object
`defineGroups`	Should groups be colored differently?
`loadings`	Should loadings be plotted instead of scores?
`legendPosition`	Where should the legend be plotted, Defaults to "left", other options include "top", "topright", etc.
`annotate`	Should loadings be annotated with metabolite identities, if available in $metadata?
`verbose`	Should a summary be displayed?
`xpd`	Should labels be clipped to the plot region (TRUE) or exceed to margins (NA)

Value

An invisible prcomp result object

Examples

results<-mrbin(silent=TRUE,setDefault=FALSE,parameters=list(dimension="2D",
    binRegion=c(8,1,15,140),binwidth2D=0.1,binheight=4,solventRegion=c(5.5,4.2),
    PQNScaling="No",noiseRemoval="Yes",trimZeros="Yes",tryParallel=TRUE,
    fixNegatives="No",logTrafo="No",PCA="No",signal_to_noise2D=10,
    NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
                 system.file("extdata/2/12/pdata/10",package="mrbin"),
                 system.file("extdata/3/12/pdata/10",package="mrbin"))))
plotPCA(results)

mrbin documentation built on June 8, 2025, 2:01 p.m.