sc.plot2d: plot2d: Plot

In genome/sciclone: Detect subclones from genomic sequence data

plot2d: Plot

Description

Creates a pdf with one plot for each pair of samples.

Usage

sc.plot2d(sco, outputFile=NULL, positionsToHighlight=NULL,
                 highlightsHaveNames=FALSE, overlayClusters=TRUE,
                 overlayErrorBars=FALSE, ellipse.metadata = list(),
                 singlePage=FALSE, scale=1, xlim=100, ylim=100,
                 plot.title=NULL, samplesToPlot=NULL,
                 clusterLegend=TRUE, 
                 flipSamples=FALSE, xlab=NULL,
                 ylab=NULL, colors=NULL,
                 plotWidth=7.2, plotHeight=6)

Arguments

sco	an scObject object created by the sciClone() function
outputFile	path/name of pdf file that will contain the plots. Optional, but generally recommended, especially if you have more than two samples
samplesToPlot	a list of sample names that should be included in the 2d plots. Default is to plot allcombinations of all samples.
overlayClusters	boolean argument to decide whether to overlay cluster designations on the standard scatterplot output
overlayErrorBars	boolean argument to decide whether to overlay (binomial) error bars on VAFs
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.
ellipse.metadata	description of ellipses for plotting cluster std errors/deviations
singlePage	If true, condenses all output plots onto a single page.
scale	scale the spacing of the plots and fonts up or down to produce output suitable for presentations (try 1.0) or print (try 2.0).
xlim	max value of the xaxis
ylim	max value of the yaxis
plot.title	Set a new title that will be applied to all plots. The default is to add a title with format "sampleNameA vs sampleNameB" to each plot
xlab	label for the x axis
ylab	label for the y axis
colors	provide your own list of colors to use for the clusters
flipSamples	flip the samples being plotted on each axis (x moves to y and vice-versa)
clusterLegend	add a legend showing cluster numbers (TRUE/FALSE)
plotWidth	width of the pdf (in inches) that is produced (default 7.2)
plotHeight	height of the pdf (in inches)that is produced (default 6)

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 or output plot

Examples

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

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