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