plot_degree: A function to plot degree distributions

In melmasri/HPprediction: Host-parasite prediction based on phylogeny

Description

This function generates a degree distribution plot for the binary interaction matrix 'Z'. Optionally, you can compare the observed matrix to the posterior matrix by including it as 'Z_est'. By default the function plots the degree for both rows (hosts) and columns (parasites), but you can modify this with the parameter 'type'.

Usage

plot_degree(
  Z,
  Z_est,
  type = "both",
  host.col = "blue",
  parasite.col = "red",
  cex.lab = 1.5,
  cex.axis = 2,
  pt.cex = 1.5,
  legend.cex = 2
)

Arguments

Z	bipartite interaction matrix
Z_est	the posterior bipartite interaction matrix (optional)
type	whether to plot 'hosts', 'parasites', or 'both'
host.col	Colour to use for hosts (default is 'blue')
parasite.col	Colour to use for parasites (default is 'red')

Examples

# Simluate a Z matrix and plot the degree distributions
## Not run: 
Z <- matrix(rbinom(50*200, 1, 0.01), nrow=50, ncol=200)
Z <- Z[,colSums(Z)>0]
plot_degree(tree)
 
## End(Not run)

melmasri/HPprediction documentation built on May 2, 2020, 11:09 a.m.