plot-gene-network: Plot a gene network graph

In kkmann/pwcuratr: Functional Pathway Cluster Curation tool

Description

Plot a gene network graph

Plot a gene network graph

Usage

plot_graph(
  igraph,
  seed_genes,
  title = NULL,
  titlesize = 10,
  textsize = 3,
  pointsize = 1,
  edgesize = 0.5,
  layout = "stress",
  layout_args = list()
)

plot_pathway(genes, seed_genes, minscore = 0, titlesize = 10, minnodes = 1)

Arguments

igraph	an igraph object as returned by as_igraph()
seed_genes	character vector of ENSEMBL IDs of the seed genes in the igraph object
title	plot title
titlesize	text size for the title
textsize	text size for labels
pointsize	point size
edgesize	edge strength
layout	ggraph layout
layout_args	list of argments to pass to ggraph layout function
genes	character vector of ensembl IDs of the genes in the network
minscore	minimal evidence score for edges to include (see as_igraph())
minnodes	minimal number of nodes in component to include in plot

Value

a ggplot object

Examples

gr <- as_igraph(c("ENSG00000130203", "ENSG00000189058"),  0.9)
plot_graph(gr, c("ENSG00000130203"))

plot_pathway(
    c("ENSG00000130203", "ENSG00000189058"),
    c("ENSG00000130203", "ENSG00000189058"),
    0.9
)

kkmann/pwcuratr documentation built on March 7, 2020, 2 a.m.