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)