plot.phyloscaled: Phylogenetic visualization of heterogenity in discrete...

In coleoguy/evobir: Evolutionary Biology in R

Phylogenetic visualization of heterogenity in discrete character evolution

Description

This function provides two methods for visualizing a phyloscaled tree produced by scaleTreeRates.

Usage

## S3 method for class 'phyloscaled'
plot(tree, method = "multiply", palette = "RdYlGn",
     edge.width = 1, cex = 1, show.tip.label = T)

Arguments

tree	a tree of class phylo and phyloscaled
method	a string describing the method to be used for visualization. Can either be "multiply" or "color", see Details
palette	a string giving the palette to be used for edge coloring, only taken into account if method = "color". See Details
edge.width	numeric value that determines branch width
cex	numeric value for size
show.tip.label	logical indicating whether to print tip labels

Details

The two plotting methods currently supported are "multiply" and "color".

multiply takes the length of each edge on the phylogeny and multiplies it by the scalar associated with the edge before plotting the scaled tree.

color assigns a color from a diverging palette to each edge depending on it's associated scalar. Currently supported palettes are any of the RColorBrewer palettes or the standard viridis palette (specified by string "viridis"). Because RColorBrewer sets the maximum number of distinct colors for divergent palettes to be 11, any phylogeny which has greater than 11 unique scalar bins represented within it's edges must use a viridis palette. The ultrametric phylogeny is then plotted with each edge colored accordingly

Value

A plotted phylogeny with edges either multiplied or colored by their associated scalars

Author(s)

Maximos Chin and Heath Blackmon

References

http://coleoguy.github.io/

See Also

scaleTreeRates

coleoguy/evobir documentation built on May 8, 2024, 6:57 p.m.