transcriptRegionOverlapsPlot: UpSet-plot to that shows the transcript region overlaps

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

UpSet-plot to that shows the transcript region overlaps

Description

A diagnostic function that plots the transcript regions of binding sites on overlapping loci. The function assignToTranscriptRegions is expected to be executed prior to calling this plot function.

Usage

transcriptRegionOverlapsPlot(object, text.size = NULL, show.title = TRUE)

Arguments

object	a BSFDataSet object
text.size	numeric; fontsize of all numbers on axis
show.title	logical; if plot title should be visible

Value

a plot of type ggplot

See Also

assignToTranscriptRegions transcriptRegionSpectrumPlot

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])
load(list.files(files, pattern = ".rds$", full.names = TRUE)[2])
bds = makeBindingSites(object = bds, bsSize = 9)
bds = assignToGenes(bds, anno.genes = gns)
bds = assignToTranscriptRegions(object = bds, anno.transcriptRegionList = regions)
transcriptRegionOverlapsPlot(bds)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.