sc.plot2dWithMargins: plot2d: Plot

In genome/sciclone: Detect subclones from genomic sequence data

plot2d: Plot

Description

Creates a pdf where each page has a scatterplot for each pair of samples along with a pair of adjacent histograms for each sample.

Usage

sc.plot2dWithMargins(sco, outputFile, positionsToHighlight=NULL,
highlightsHaveNames=FALSE, overlayErrorBars=FALSE)

Arguments

sco	an scObject object created by the sciClone() function
outputFile	path/name of pdf file of plots to create
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 label these points on the plot.
overlayErrorBars	boolean argument to decide whether to overlay (binomial) error bars on VAFs

Details

Creates a scatter plot for each pairing of samples, with clusters indicated by color and shape.

Value

does not return anything, creates pdf file

Examples

  # sc.plot2d(sc,"results/clusters.2d.pdf")

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