plotRecurrence: panConusig::plotRecurrence

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

panConusig::plotRecurrence

Description

Plot recurrence of copy number signature across the genome, labelling genes of interest or chromosome arms that show highly recurrent signature attribution.

Usage

plotRecurrence(props,counts,tumTypes,windows,
arms,doGenes=FALSE,doArms=TRUE,plotGenes=TRUE,outDir="~/",
filename=NULL,whichSigs="CN19",
colours = c("red","blue","green","black","gray","orange","cyan","purple"),
whichGenes="CN19",genesToTest="MDM2",propThreshold=0.2,countThreshold=5,
ensembl=NULL,splits=NA,mids=NA,saveRes=FALSE,geneGR=NULL,windowGR=NULL,
doCombine=TRUE,doSex=FALSE,doLegend=TRUE,
doMain=TRUE,LTY=1:5,YLIM=NULL,LABY=NULL,
offsetBase=0.01,offsetTweak=0.02,xoverlap=100,
yoverlap=0.02,myMAR=NULL,XLIMadj=0,
geneCex=2,legloc="topright",doGenesAbove=TRUE,
mylayout=NULL,ylineoffset=NULL,
pdfWidth=21,pdfHeight=7,CEX=4,doSplit=FALSE,legnames=NULL,propArm=0.75,
geneYtweak=0,extraMain=NULL)

Arguments

props	Matrix of proportions of signature recurrence across genomic bins. See getRecurrence().
counts	Matrix of counts of signature recurrence across genomic bins. See getRecurrence().
tumTypes	Vector of tumour types for each sample.
windows	Genomic windows that were used to generate props and counts. See setupWindows().
arms	Chromosome arm information for plotting labels of recurrent signatures at an arm/chromosome level. See loadCytoband().
doGenes	Whether to calculate gene names of genes overlapping regions of recurrence.
doArms	Whether to plot chromosome arm names of arms overlapping regions of recurrence.
plotGenes	Whether to plot gene names of genes overlapping regions of recurrence.
outDir	Directory for saving plot as pdf.
filename	Filename for saving plot as pdf. If NULL no pdf will be produced.
whichSigs	Vector of signature names to plot.
colours	Vector of colours for each signature.
whichGenes	Vector of signature names for which to plot gene names.
genesToTest	Vector of gene names to consider plotting.
propThreshold	Proportion threshold above which to plot gene/arm labels.
countThreshold	Count threshold above which to plot gene/arm labels.
ensembl	Biomart ensembl object to look up gene coordinates. If NULL, geneGR and whichGenes will be used instead.
splits	Index of windows that split separate chromosomes. See setupWindows().
mids	index of windows that mark the midpoints of chromosomes. See setupWindows().
saveRes	Boolean. Whether to save the window and recurrence information as a csv.
geneGR	GenomicRanges object denoting genomic positions of genes listed in genesToTest.
windowGR	GenomicRanges object denoting genomic windows in which recurrence has been evaluated. See setupWindows().
doCombine	Output of getRecurrence is sometimes a list. If so, doCombine=TRUE will convert to a matrix internally.
doSex	Boolean. Whether to plot sex chromosomes.
doLegend	Boolean. Whether to plot a legend.
doMain	Boolean. Whether to plot title.
LTY	Vector of line types for each signature to be plotted.
YLIM	Custom values for plotting y-axis limits.
LABY	Custom label for the y-axis.
offsetBase	Y offset for plotting gene labels.
offsetTweak	X offset for plotting gene labels.
xoverlap	Overlap required for automated moving of overlapping gene labels (x-axis).
yoverlap	Overlap required for automated moving of overlapping gene labels (y-axis).
myMAR	Custom margins for plotting.
XLIMadj	Extension to the right hand xlim value.
geneCex	cex value for plotting gene labels.
legloc	Location for legend.
doGenesAbove	Boolean. Whether to plot gene names on plot (FALSE), or ina separate panel above the plot (TRUE).
mylayout	Custom layout for multi-panel figure (When doGenesAbove==TRUE).
ylineoffset	Offset for lines connecting gene names to plot.
pdfWidth	Width for output pdf.
pdfHeight	Height for output pdf.
CEX	cex value for plot text.
doSplit	Boolean. Whether to split plot into two panels (Only use when plotting two signatures).
legnames	Names for legens.
propArm	Proportion of chromosome arm that must be above propThreshold to plot arm label.
geneYtweak	Offset for plotting gene labels (y-axis).
extraMain	Subtitle.

Value

Pdf if filename is not NULL, csv if saveRes is not FALSE.

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