sc.plot2d | R Documentation |
Creates a pdf with one plot for each pair of samples.
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)
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) |
Creates a scatter plot for each pairing of samples, with clusters indicated by color and shape.
does not return anything, creates pdf file or output plot
# sc.plot2d(sc,"results/clusters.2d.pdf")
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