plot.phyloregion function

Visualize biogeographic patterns

## S3 method for class 'phyloregion'
plot(x, pol = NULL, palette = "NMDS", col = NULL, label = FALSE, ...)

plot_NMDS(x, ...)

text_NMDS(x, ...)

Arguments

• x: an object of class phyloregion from phyloregion
• pol: a polygon shapefile of grid cells.
• palette: name of the palette to generate colors from. The default, NMDS , allows display of phyloregions in multidimensional scaling color space matching the color vision of the human visual system. The name is matched to the list of available color palettes from the hcl.colors function in the grDevices package.
• col: vector of colors of length equal to the number of phyloregions.
• label: Logical, whether to print cluster names or not
• ...: arguments passed among methods.

Returns

No return value, called for plotting.

Examples

library(terra)
data(africa)
tree <- africa$phylo
x <- africa$comm
p <- vect(system.file("ex/sa.json", package = "phyloregion"))

subphy <- match_phylo_comm(tree, x)$phy
submat <- match_phylo_comm(tree, x)$com

pbc <- phylobeta(submat, subphy)
y <- phyloregion(pbc[[1]], pol=p)

plot_NMDS(y, cex=6)
text_NMDS(y, cex=2)
plot(y, cex=1, palette="NMDS")
plot(y, cex=1)