plot.phyloregion: Visualize biogeographic patterns

Description Usage Arguments Value Examples

View source: R/visualize_phyloregions.R

Description

Visualize biogeographic patterns

Usage

1
2
3
4
5
6
## S3 method for class 'phyloregion'
plot(x, shp = NULL, palette = "NMDS", col = NULL, ...)

plot_NMDS(x, ...)

text_NMDS(x, ...)

Arguments

x

an object of class phyloregion from phyloregion

shp

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.

...

arguments passed among methods.

Value

No return value, called for plotting.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
data(africa)
tree <- africa$phylo
x <- africa$comm

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

pbc <- phylobeta(submat, subphy)
y <- phyloregion(pbc[[1]], shp=africa$polys)

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

phyloregion documentation built on May 1, 2021, 9:06 a.m.