plotPCA {mrbin} | 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
resetEnv()#clean up previous data from the package environment
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",
fixNegatives="No",logTrafo="No",PCA="No",signal_to_noise2D=10,
example=TRUE,#only used for the package examples
NMRfolders=c(system.file("extdata/1.mr2",package="mrbin"),
system.file("extdata/2.mr2",package="mrbin"),
system.file("extdata/3.mr2",package="mrbin")),
NMRvendor="mrbin"))
plotPCA(results)
[Package mrbin version 1.9.4 Index]