Plot a gene network graph

Source: R/plot_pathway.R

Plot a gene network graph

Plot a gene network graph

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
)