In TomKellyGenetics/plot.igraph: Extensions to iGraph for custom plots

Install

library("igraph")
library("devtools")
devtools::install_github("TomKellyGenetics/plot.igraph")
library("plot.igraph")

Set up simulated graph

graph_edges <- rbind(c("A", "C"), c("B", "C"), c("C", "D"), c("D", "E"), c("D", "F"), c("F", "G"), c("F", "I"), c("H", "I"))
graph <- graph.edgelist(graph_edges, directed = T)

Plotting

plot_directed with default settings uses the layout.fruchterman.reingold as does the default igraph::plot.igraph.

plot(graph)
plot_directed(graph)

plot_directed supports customised layouts and colours:

plot_directed(graph, layout = layout.kamada.kawai)
plot_directed(graph, fill.node = "lightblue", border.node = "royalblue")

Colours may also be entered as a vector for each node in V(graph):

names(V(graph))
colour_vector <- ifelse(names(V(graph)) %in% c("A", "D", "I"), 1, 2)
plot_directed(graph, fill.node = c("lightblue", "grey")[colour_vector], border.node = c("royalblue", "black")[colour_vector])

Arrow customisation

The state parameter controls whether the links are "activating" or "inhibiting". These may be applied globally as a character or numeric:

Activating links

• "activating"
• 1
• 0

Inhibiting links

• "inhibiting"
• -1
• 2

plot_directed(graph, state = "activating")
plot_directed(graph, state = "inhibiting")
plot_directed(graph, state = 1)
plot_directed(graph, state = -1)
plot_directed(graph, state = 0)
plot_directed(graph, state = 2)

Vectorisation

The state parameter may also apply as a vector to each edge in E(graph) respectively.

E(graph)
plot_directed(graph, state = c(1, 1, -1, -1, 1, -1, 1, -1))

TomKellyGenetics/plot.igraph documentation built on April 8, 2020, 2:46 p.m.