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Plot a relationship graph (RG)

Source: R/plot_RG.R
plot_RG.Rd

This function is a wrapper around plot.igraph, written to group parasite genotypes by episode both spatially and using vertex colour (specifically, parasite genotypes within episodes are vertically distributed with some horizontal jitter when layout.by.group = TRUE (default), and equicolored), and to ensure clone and sibling edges are plotted using different line types.

Usage

plot_RG(
  RG,
  layout.by.group = TRUE,
  vertex.palette = "Set2",
  edge.lty = c(sibling = "dashed", clone = "solid"),
  edge.col = c(sibling = "black", clone = "black"),
  edge.width = 1.5,
  ...
)

Arguments

RG

igraph object encoding an RG; see RG_to_igraph.

layout.by.group

Logical; if TRUE (default) overrides the default layout of plot.igraph so that vertices that represent parasite genotypes from different episodes are distributed horizontally and vertices that represent genotypes within episodes are distributed vertically.

vertex.palette

A character string specifying an RColorBrewer palette. Overrides the default palette of plot.igraph.

edge.lty

Named vector of edge line types corresponding to different relationships.

edge.col

Named vector of edge colours corresponding to different relationships.

edge.width

Overrides the default edge.width of plot.igraph.

...

Additional arguments to pass to plot.igraph, e.g., edge.curved.

Value

None

Details

To see how to plot relationship graphs outputted by compute_posterior, please refer to Exploration of relationship graphs in Demonstrate Pv3Rs usage .

Provenance

This function was adapted from plot_Vivax_model at https://github.com/jwatowatson/RecurrentVivax/blob/master/Genetic_Model/iGraph_functions.R.

Examples

RGs <- enumerate_RGs(c(2, 1, 1), progress.bar = FALSE)
#> Number of valid relationship graphs (RGs) is 48
oldpar <- par(no.readonly = TRUE) # record user's options
par(mfrow = c(3, 4), mar = c(0.1, 0.1, 0.1, 0.1))
for (i in 12:23) {
  plot_RG(RGs[[i]],
  edge.col = c(sibling = "gray", clone = "black"),
  edge.lty = c(sibling = "dotted", clone = "solid"),
  edge.curved = 0.1)
  box()
}

par(oldpar) # restore user's options