plotInteractionAnnotations: Plot a donut plot of interaction types for an annotated...

In ComputationalRegulatoryGenomicsICL/GenomicInteractions-new: Utilities for handling genomic interaction data

Plot a donut plot of interaction types for an annotated GInteractions object

Description

Plot a donut plot of interaction types for an annotated GInteractions object

Usage

plotInteractionAnnotations(
  GIObject,
  node.classes = NULL,
  viewpoints = NULL,
  other = 0,
  keep.order = FALSE,
  legend = FALSE
)

Arguments

GIObject	A GInteractions object
node.classes	Optional. All node.classes to include in the analysis. Default: all node classes.
viewpoints	Optional. If set will only consider interactions where at least one anchor is of this node class. Default: all classes in node.classes.
other	Optional. Interaction types making up fewer than 'other' percent of the total interactions will be consolidated into a single 'other' category.
keep.order	Optional. Logical. Keep original order of node.classes for plotting or not. Default: FALSE, alphabetical order.
legend	Optional. Logical. If TRUE, legend is plotted to right of donut plot. If FALSE, donut plot is annotated with category names.

Value

A ggplot2 plot

Examples

library('GenomicRanges')
data(hic_example_data)
data(mm9_refseq_promoters)
mm9_refseq_grl = split(mm9_refseq_promoters, mm9_refseq_promoters$id)
annotateInteractions(hic_example_data, list(promoter=mm9_refseq_grl))
plotInteractionAnnotations(hic_example_data)

ComputationalRegulatoryGenomicsICL/GenomicInteractions-new documentation built on April 10, 2022, 5:39 p.m.