plotInteractionAnnotations: Plot interaction types

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Plot a donut plot of interaction types for an annotated GenomicInteractions object.

Usage

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

Arguments

GIObject	A GenomicInteractions object
node.classes	Character vector specifying the node classes to include in the plot. Defaults to all available node classes.
viewpoints	Character vector of acceptable node classes, where interactions are only considered if least one anchor is of an acceptable node class. Defaults to all classes in node.classes.
other	Numeric scalar of the minimum proportion for an interaction type to be shown. Interaction types making up fewer than other percent of the total interactions will be consolidated into a single “other” category.
keep.order	Logical scalar specifying whether the original order of node.classes should be retained for plotting. Default is to use the alphabetical order.
legend	Logical scalar specifying whether the legend should be plotted. If FALSE, donut plot is annotated with category names.

Value

A ggplot2 plot.

Examples

library("GenomicRanges")
data(hic_example_data)
hic_example_data <- updateObject(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)

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.