Visualize biogeographic patterns

# S3 method for 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.

Value

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)
#> Warning: convex combination of colors in polar coordinates (polarLUV) may not be appropriate
#> Warning: convex combination of colors in polar coordinates (polarLUV) may not be appropriate

plot_NMDS(y, cex=6)
#> Warning: convex combination of colors in polar coordinates (polarLUV) may not be appropriate
#> Warning: convex combination of colors in polar coordinates (polarLUV) may not be appropriate
text_NMDS(y, cex=2)

plot(y, cex=1, palette="NMDS")
plot(y, cex=1)