plotNetworkFromMatrix: Plot graphs from adjacency matrices

In eicm: Explicit Interaction Community Models

Plot graphs from adjacency matrices

Description

Plots a graph from a weighted adjacency matrix, using igraph's plotting functions, optionally comparing it with another "true" adjacency matrix.

Usage

plotNetworkFromMatrix(
  adjacency,
  true.adjacency = NULL,
  labels = TRUE,
  exclude.orphans = TRUE,
  lwd = 1,
  edge.arrow.size = 0.8,
  severe.threshold = 0.5
)

Arguments

adjacency	the square adjacency matrix.
true.adjacency	optional. The reference "true" square adjacency matrix to which to compare the first one.
labels	logical. Draw default labels?
exclude.orphans	logical. Hide nodes without links?
lwd	a numerical value giving the amount by which the arrows' line width should be magnified relative to the default, when plotting the weighted graph (only used when true.adjacency is not provided).
edge.arrow.size	size of the arrow heads. See igraph::plot.igraph
severe.threshold	the absolute threshold above which the interaction weights are highlighted in the graph.

Details

When comparing two adjacency matrices

Value

The corresponding igraph network, invisibly.

Note

The arrow direction depicts the direction of the interaction. Species in columns affect species in rows.

The matrices should include row and column labels, otherwise the node labels may not correspond to the species index (when exclude.orphans = TRUE)

Examples

# generate two adjacency matrices with 15 species and 10 interactions
A <- matrix(0, ncol=15, nrow=15)
A[sample(length(A), 10)] <- runif(10)

B <- matrix(0, ncol=15, nrow=15)
B[sample(length(B), 10)] <- runif(10)

# set the species names
rownames(A) <- rownames(B) <-
  colnames(A) <- colnames(B) <- paste0("S", 1:15)

plotNetworkFromMatrix(A, B)

eicm documentation built on May 31, 2023, 5:20 p.m.