plotSigDefinitions: panConusig::plotSigDefinitions

In UCL-Research-Department-of-Pathology/panConusig: Pan-cancer copy number signatures analysis

panConusig::plotSigDefinitions

Description

Generates barplots of signature definitions.

Usage

plotSigDefinitions(sigs,sigLength=2,doTitle=TRUE,doTitleBar=FALSE,doText=FALSE,
                               doYlab=TRUE,doLab=FALSE,ncol=1,nPerCol="all",plotBars=c(1,2),
                               myMAR=NULL,barSize=1.15,returnLayout=FALSE,myLayout=NULL,CEX=1.8,
                               YLIM=NULL,mainAdj=0.5,mainLine=0,doBox=FALSE,HDlab="",
                               extraLabel=NULL,extraAdj=0.5,extraAt=15,extraCex=0.5)

Arguments

sigs	Matrix. 48xn matrix of signature definitions, where n is the number of signatures
sigLength	Signature plot width to be specified in layout. Integer.
doTitle	Whether to plot signature names as a title.
doTitleBar	Whether to plot copy number classes as coloured bars.
doText	Whether to add copy number class labels as text in coloured bars..
doYlab	Whether to plot signature names as y-axis labels.
doLab	Whether to plot segment size classes as x-axis labels.
ncol	Number of columns to plot signatures in.
nPerCol	Number of signatres per column to plot.
plotBars	Vector of any combination of c(1,2). If 1 is in plotBars, coloured bars will be plotted above signatures. If 2 is in plotBars, coloured bars will be plotted below signatures.
myMAR	Custom margins.
barSize	Size for coloured bars.
returnLayout	Boolean. Whether to return the layout matrix used for plotting.
myLayout	Custom layout for plotting.
YLIM	Custom y-axis limits.
mainAdj	X-axis adjustment for signature title.
mainLine	y-axis line for signature title.
doBox	Boolean. Whether to surround each signature definition with a box.
HDlab	Label to use for homozygous deletions.
extraLabel	Label for signature subtitle.
extraAdj	Adjustment for signature subtitle.
extraAt	Position for signature subtitle.
extraCex	cex for signature subtitle.

Value

Matrix of layout used if returnLayout==TRUE.

UCL-Research-Department-of-Pathology/panConusig documentation built on March 25, 2022, 12:18 a.m.