plotPartitions: Produces a barplot showing how query regions of interest are...

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Produces a barplot showing how query regions of interest are distributed across a given partition list

Description

This function can be used to test a GRanges object against any arbitrary list of genome partitions. The partition list is a priority-ordered list of GRanges objects. Each region in the query will be assigned to a given partition that it overlaps with the highest priority.

Usage

plotPartitions(assignedPartitions, numbers = FALSE, stacked = FALSE)

Arguments

assignedPartitions	A table holding the frequency of assignment to each of the partitions. Produced by calcPartitions
numbers	logical indicating whether raw overlaps should be plotted instead of the default percentages
stacked	logical indicating that data should be plotted as stacked bar plot

Value

A ggplot object using a barplot to show the distribution of the query regions across a given partition list.

Examples

p = calcPartitionsRef(vistaEnhancers, "hg19")
partPlot = plotPartitions(p)
partCounts = plotPartitions(p, numbers=TRUE)
partPlot = plotPartitions(p, stacked=TRUE)

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.