plotPCA: A function for plotting PCA plots.

In mrbin: Metabolomics Data Analysis Functions

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
)

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?

Value

An invisible prcomp result object

Examples

mrbinResults<-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=FALSE,
    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"))))
plotPCA(mrbinResults)

mrbin documentation built on Jan. 23, 2023, 5:41 p.m.