sgraph-methods: Extract a splicing graph as a plottable graph-like object

In Bioconductor/SplicingGraphs: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Extract a splicing graph as a plottable graph-like object

Description

Extract the splicing graph for a given gene from a SplicingGraphs object and return it as a plottable graph-like object.

Usage

sgraph(x, keep.dup.edges=FALSE, tx_id.as.edge.label=FALSE, as.igraph=FALSE)

## PLotting:

## S4 method for signature 'SplicingGraphs,missing'
plot(x, y, ...)
slideshow(x)

Arguments

x	TODO
keep.dup.edges	If FALSE (the default), then edges with the same global edge id are merged together. Use keep.dup.edges=TRUE if this merging should not be performed.
tx_id.as.edge.label	Whether or not to use the transcript ids as edge labels.
as.igraph	TODO
y	TODO
...	Additional arguments. plot passes these to plot,Ragraph,ANY-method for use in, e.g., adding a main title to the plot.

Details

TODO

Value

TODO

Author(s)

H. Pagès

See Also

This man page is part of the SplicingGraphs package. Please see ?`SplicingGraphs-package` for an overview of the package and for an index of its man pages.

Examples

example(SplicingGraphs)  # create SplicingGraphs object 'sg'
sg

## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids.
names(sg)

graphA <- sgraph(sg["geneA"], tx_id.as.edge.label=TRUE)

if (interactive()) {
  ## Edges are labeled with the transcript ids (or names), in blue.
  ## The orange arrows are edges corresponding to exons:
  plot(graphA)

  ## Note that plot() works directly on a SplicingGraphs object of
  ## length 1:
  plot(sg["geneB"])

  ## Slideshow of the graphs:
  slideshow(sg)
}

Bioconductor/SplicingGraphs documentation built on Nov. 3, 2024, 8:11 a.m.