plotPCA: Plots for Principle Component Analysis (PCA) in QSEA

plotPCAR Documentation

Plots for Principle Component Analysis (PCA) in QSEA

Description

The principle components can be depicted using the plotting methods plotPCA and plotPCAfactors

Usage

## S4 method for signature 'qseaPCA'
plotPCA(object,plotComponents=c(1,2), fgColor="black",
    bgColor = "white", legend, plotLabels=TRUE, radius=5, labelOffset=.5,
    labelPos=1, labelAdj, labelColor="black", cex=1, ...)

## S4 method for signature 'qseaPCA'
plotPCAfactors(object,plotComponents=c(1,2), 
    fgColor="black",bgColor = "white", plotTopLabels=100, labelsOfInterest, 
    radius=1, labelOffset=.5,labelPos=1,labelColor="black", cex=1, ...)

Arguments

object

the qseaPCA object, resulting from the getPCA function

plotComponents

vector of the two components of the PCA

fgColor

vector of foreground colors for the circles

bgColor

vector of background colors for the circles

legend

add a legend to the plot

plotLabels

if set TRUE, the labels of the samples are written in the plot

radius

defines the size of the plotted circles

labelOffset

defines the offset of the labels to the circles

labelPos

specify position of the labels in the plot (see graphics::text)

labelAdj

alternative way to specify position of the labls in the plot (see graphics::text)

labelColor

a vector of colors for the labels

cex

font size of the labels

plotTopLabels

labels of factors with strongest contribution to plotted components are shown

labelsOfInterest

vector of factor names that are highlighted and labeled in the plot

...

further graphical parameters

Value

The functions return a list with the coordinates of the depicted components

Author(s)

Mathias Lienhard

See Also

plotPCA

Examples

 
qs=getExampleQseaSet( repl=5)
pca=getPCA(qs, norm_method="beta")
colors=c(rep("red", 5), rep("green", 5))

plotPCA(pca, bgColor=colors)
#plotPCAfactors is more interesting, if ROIs have been specified in getPCA
plotPCAfactors(pca)


MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.