sc.plot1d: plot1d: Plot kernel density and copy number information for...

In genome/sciclone: Detect subclones from genomic sequence data

plot1d: Plot kernel density and copy number information for each sample

Description

Creates a pdf with one plot for each sample.

Usage

sc.plot1d(sco, outputFile=NULL, cnToPlot=c(1,2,3,4),
                showCopyNumberScatterPlots=TRUE, highlightSexChrs=TRUE,
                positionsToHighlight=NULL, highlightsHaveNames=FALSE,
                overlayClusters=TRUE, overlayIndividualModels=TRUE,
                showHistogram=FALSE, showTitle=TRUE,
                biggerText=FALSE, highlightsOnHistogram=FALSE,
                highlightCnPoints=FALSE)

Arguments

sco	an scObject object created by the sciClone() function
outputFile	path/name of plot-containing pdf file to create
cnToPlot	create a shortened plot with only the density plots and indicated cn regions (a subset of c(1,2,3,4))
showCopyNumberScatterPlots	show the scatter plots of depth and VAF
highlightSexChrs	boolean argument to decide whether or not to highlight all sex-chromosome variants using a different plotting emblem than that used for other data points (a triangle is currently used)
highlightCnPoints	boolean argument to decide whether or not to highlight all variants with chromosome specified as "CN". This is intended to be used when including pseudo-vafs from CN events detected with external methods. Points are highlighted by using a square for the plotting emblem.
positionsToHighlight	a list of positions in 2-column format 1) chromosome 2) position. These points will be highlighted on the output scatterplot by using a different character than that used for other data points
highlightsHaveNames	boolean argument - if (TRUE), the tool will look for a third column in the file specified by positionsToHighlight and will number these points, then create a legend with the names. Also sets cnToPlot=2 to make room for the legend.

overlayClusters	boolean argument to decide whether to overlay cluster designations on the standard scatterplot output
overlayIndividualModels	show the model fits for each cluster on the density plot
showHistogram	display a histogram on the density plot
showTitle	Use the sample names as the titles of the plots
biggerText	bump up the font size to make small plots legible
highlightsOnHistogram	show higlighted points on histogram

Value

does not return anything, creates pdf file

Examples

  # sc.plot1d(sc,"results/clusters.1d.pdf")

genome/sciclone documentation built on Oct. 15, 2023, 5:09 a.m.