sciClone (version 1.1.0)

sc.plot2dWithMargins: 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

Value

does not return anything, creates pdf file

Details

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

Examples

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