geneOverlapsPlot: UpSet-plot to that shows the gene type overlaps

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

UpSet-plot to that shows the gene type overlaps

Description

A diagnostic function that plots the gene types of binding sites on overlapping loci genes. The function assignToGenes is expected to be executed prior to calling this plot function.

Usage

geneOverlapsPlot(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

assignToGenes targetGeneSpectrumPlot

Examples

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

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