getFusionExpressionPlotData: Generate the plot data object for a fusion expression plot.

In jefferys/fusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Merge data from multiple genes and multiple point sets into a list for plotting as a fusion expression graph. Uses grToRect and pointToPoly. This is a lower-level function called by plotting functions like plotFusionExpressionOne or plotFusionExpressionPair

Usage

getFusionExpressionPlotData(genes, fusions, geneNames, geneSep = 500,
  fusionSep = 40, nameSep = 20)

Arguments

genes	List of genomic ranges objects to plot, by gene name.
fusions	List of vectors of genomic fusion points to plot, by gene name.
geneNames	Vector of gene names.
geneSep	Distance between genes in the plot, in bases. Default = 500.
fusionSep	Distance between exon tops and tops of plotted fusion points, in bases. Default = 40
nameSep	Distance between the plot and the gene name annotation, in bases. Default = 20.

Value

A "fusion expression plot data" object, a list with the data needed to plot the gene models, expression levels, and fusion points. This list has the folowing elements:

geneRects	The coordinates of the rectangles to plot as exons
fusionPolys	The coordinates of the polygons (triangles) used as fusion point markers
geneNames	The names of the genes being plotted
xRange	The min and max x values in the plot
yRange	The min and max y values in the plot

See Also

grToRect, pointToPoly, plotFusionExpressionOne, plotFusionExpressionPair plotFusionExpressionPlotData

jefferys/fusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.