Plot a relationship graph (RG)

This function is a wrapper around plot.igraph, written to group parasite genotypes by infection, both spatially and using vertex colour. Specifically, parasite genotypes within infections are vertically distributed with some horizontal jitter when layout_by_group is TRUE (default), and coloured the same. It also makes sure clonal and sibling edges are plotted differently using different line types.

Usage

plot_RG(
  RG,
  layout_by_group = TRUE,
  vertex_palette = "Set2",
  edge_lty = c(`0.5` = "dashed", `1` = "solid"),
  edge_col = c(`0.5` = "black", `1` = "black"),
  edge_width = 1.5,
  ...
)

Arguments

RG

A relationship graph, which is an igraph graph; see return value of RG_to_igraph.

layout_by_group

A logical argument which if TRUE (default) overrides the default layout of plot.igraph so that vertices that represent parasite genotypes from different infections are distributed horizontally and vertices that represent genotypes within infections are distributed vertically.

vertex_palette

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

edge_lty

A vector of edge line types corresponding to different relationships, where 0.5 represents a sibling and 1 represents a clone.

edge_col

A vector of edge colours corresponding to different relationships, where 0.5 represents a sibling and 1 represents a clone.

edge_width

Overrides the default edge.width of plot.igraph.

...

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

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))
#> Number of valid relationship graphs (RGs) is 48
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cpar <- par() # record current par before changing
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.curved = 0.1)
  box()
}

par(cpar) # reset par
#> Warning: graphical parameter "cin" cannot be set
#> Warning: graphical parameter "cra" cannot be set
#> Warning: graphical parameter "csi" cannot be set
#> Warning: graphical parameter "cxy" cannot be set
#> Warning: graphical parameter "din" cannot be set
#> Warning: graphical parameter "page" cannot be set