plot.SciClone: plot.SciClone: Plot kernel density and copy number...
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments Value Examples

Creates a pdf with one plot for each sample.

plot.SciClone(sco, outputFile, 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)

`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)
`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