plot_netassoc_network: Plots species association network

In bblonder/netassoc: Inference of Species Associations from Co-Occurrence Data

Plots species association network

Description

Draws a network of species associations. By default edge widths are proportional to association strength and edge color reflects association type (blue, positive; red, negative).

Usage

plot_netassoc_network(network, layout = layout_nicely(network), 
  vertex.label = V(network)$name, 
  vertex.color = NA, 
  vertex.shape = "none",
  vertex.label.color = "black", 
  vertex.label.family = "sans",
  edge.width = NULL, 
  edge.color = NULL, 
  edge.arrow.size = 0.2, 
  vertex.label.cex = 0.5, 
  legend = TRUE,
   ...)

Arguments

network	An igraph object corresponding to the association network
layout	Graphical layout. See igraph::layout.
vertex.label	String labels for species.
edge.width	Edge widths for links between species.
edge.color	Edge colors for links between species.
vertex.color	Vertex colors for species.
vertex.label.color	Vertex label colors for species.
vertex.shape	Vertex shape for species.
edge.arrow.size	Edge arrow size for links between species.
vertex.label.cex	Vertex label expansion factor for species.
vertex.label.family	Vertex shape font family for species.
legend	If TRUE, plots a scale legend.
...	Other arguments to be passed to plot.igraph.

Examples

# generate random data
set.seed(5)
nsp <- 10
nsi <- 5
m_obs <- floor(matrix(rgamma(nsp*nsi,shape=5),ncol=nsi,nrow=nsp))
m_nul <- floor(matrix(rexp(nsp*nsi,rate=0.05),ncol=nsi,nrow=nsp))

n <- make_netassoc_network(m_obs, m_nul, numnulls=100, plot=TRUE,alpha=0.5)

# plot
plot_netassoc_network(n$network_all)

# plot using circular layout
plot_netassoc_network(n$network_all, layout=layout.circle(n$network_all))

bblonder/netassoc documentation built on July 22, 2022, 3:10 a.m.