plot_directed: Extensions to igraph for Customising plots

In TomKellyGenetics/graphsim: Simulate Expression Data from 'igraph' Networks

Extensions to igraph for Customising plots

Description

Functions to plot_directed or graph structures including customised colours, layout, states, arrows. Uses graphs functions as an extension of igraph. Designed for plotting directed graphs.

Usage

plot_directed(
  graph,
  state = NULL,
  labels = NULL,
  layout = layout.fruchterman.reingold,
  cex.node = 1,
  cex.label = 0.75,
  cex.arrow = 1.25,
  cex.main = 0.8,
  cex.sub = 0.8,
  arrow_clip = 0.075,
  pch = 21,
  border.node = "grey33",
  fill.node = "grey66",
  col.label = NULL,
  col.arrow = NULL,
  main = NULL,
  sub = NULL,
  xlab = "",
  ylab = "",
  frame.plot = F
)

Arguments

graph	An igraph object. Must be directed with known states.
state	character or integer. Defaults to "activating" if no "state" edge attribute found. May be applied a scalar across all edges or as a vector for each edge respectively. Accepts non-integer values for weighted edges provided that the sign indicates whether links are activating (positive) or inhibiting (negative). May also be entered as text for "activating" or "inhibiting" or as integers for activating (0,1) or inhibiting (-1,2). Compatible with inputs for make_state_matrix or generate_expression_graph in the graphsim package https://github.com/TomKellyGenetics/graphsim. Vector input is supported
labels	character vector. For labels to plot nodes. Defaults to vertex names in graph object. Entering "" would yield unlabelled nodes.
layout	function. Layout function as selected from layout_. Defaults to layout.fruchterman.reingold. Alternatives include layout.kamada.kawai, layout.reingold.tilford, layout.sugiyama, and layout.davidson.harel. A 2-column layout matrix giving x and y co-ordinates of each node can be given.
cex.node	numeric. Defaults to 1.
cex.label	numeric. Defaults to 0.75.
cex.arrow	numeric Defaults to 1.25. May take a scalar applied to all edges or a vector with values for each edge respectively.
cex.main	numeric. Defaults to 0.8.
cex.sub	numeric. Defaults to 0.8.
arrow_clip	numeric Defaults to 0.075 (7.5%).
pch	parameter passed to plot. Defaults to 21. Recommends using selecting between 21-25 to preserve colour behaviour. Otherwise entire node will inherit border.node as it's colour, in which case a light colour is recommended to see labels.
border.node	character. Specifies the colours of node border passed to plot. Defaults to grey33. Applies to whole node shape if pch has only one colour.
fill.node	character. Specfies the colours of node fill passed to plot. Defaults to grey66.
col.label	character. Specfies the colours of node labels passed to plot. Defaults to par("fg").
col.arrow	character. Specfies the colours of arrows passed to plot. Defaults to par("fg"). May take a scalar applied to all edges or a vector with colours for each edge respectively.
main, sub, xlab, ylab	Plotting parameters to specify plot titles or axes labels
frame.plot	logical. Whether to frame plot with a box. Defaults to FALSE.

Value

base R graphics

Author(s)

Tom Kelly [e-mail]

See Also

See also generate_expression for computing the simulated data, make_sigma for computing the Sigma (Σ) matrix, make_distance for computing distance from a graph object, make_state for resolving inhibiting states.

See also heatmap.2 for plotting matrices.

See also make_laplacian, make_commonlink, or make_adjmatrix for computing input matrices.

See also igraph for handling graph objects and plot.igraph for base R plot methods.

Other graphsim functions: generate_expression(), make_adjmatrix, make_commonlink, make_distance, make_laplacian, make_sigma, make_state

Examples

# generate example graphs
library("igraph")
graph_structure_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_structure <- graph.edgelist(graph_structure_edges, directed = TRUE)

# plots with igraph defaults
plot(graph_structure, layout = layout.fruchterman.reingold)
plot(graph_structure, layout = layout.kamada.kawai)

# plots with scalar states
plot_directed(graph_structure, state="activating")
plot_directed(graph_structure, state="inhibiting")

# plots with vector states
plot_directed(graph_structure, state = c(1, 1, 1, 1, -1, 1, 1, 1))
plot_directed(graph_structure, state = c(1, 1, -1, 1, -1, 1, -1, 1))
plot_directed(graph_structure, state = c(1, 1, -1, 1, 1, 1, 1, -1))

# plots states with graph attributes
E(graph_structure)$state <- 1
plot_directed(graph_structure)
E(graph_structure)$state <- c(1, 1, -1, 1, -1, 1, -1, 1)
plot_directed(graph_structure)

# plot layout customised
plot_directed(graph_structure, state=c(1, 1, -1, 1, -1, 1, -1, 1), layout = layout.kamada.kawai)

TomKellyGenetics/graphsim documentation built on Sept. 17, 2022, 1:37 a.m.