plot.phyloregion: Visualize biogeographic patterns

In phyloregion: Biogeographic Regionalization and Macroecology

Visualize biogeographic patterns

Description

Visualize biogeographic patterns

Usage

## 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.

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)

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

phyloregion documentation built on Aug. 15, 2023, 9:07 a.m.