Plot a phylospatial object

Plot a phylospatial object

Usage

# S3 method for class 'phylospatial'
plot(x, y = c("tree", "comm"), taxa = NULL, max_taxa = 12, ...)

Arguments

x

phylospatial object

y

Either "tree" or "comm", indicating which component to plot.

taxa

Optional vector specifying which lineage ranges to plot if y = "comm". Either a character vector of lineage names (column names of x$comm, i.e. tip labels for terminal taxa and "clade1", "clade2", etc. for larger clades) or an integer vector of column indices of x$comm (which correspond to the edges of x$tree). Ranges are plotted in the order given. If NULL (the default), a random sample of up to max_taxa lineages is plotted.

max_taxa

Integer giving the maximum number of randomly selected lineage ranges to plot if y = "comm" and taxa is NULL. Ignored if taxa is provided.

...

Additional arguments passed to plotting methods, depending on y and the class of x$spatial. For y = "tree", see plot.phylo; for y = "comm", see plot or plot.sf.

Value

A plot of the tree or community data.

Examples

ps <- ps_simulate(20, 20, 20)
plot(ps, "tree")

plot(ps, "comm")


# plot specific lineages, by name or by index
plot(ps, "comm", taxa = c("t1", "t2", "clade1"))

plot(ps, "comm", taxa = 1:4)