GenomicInteractions (version 1.6.2)

plotInteractionAnnotations: 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)