plot_RG: Plot a relationship graph (RG)

Description

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,
  ...
)

Value

None

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.

Details

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

{demonstrate-usage}{exploration-of-relationship-graphs}{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.

RGs <- enumerate_RGs(c(2, 1, 1), progress.bar = FALSE) 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