Plot.phylocl: Plot phylogenetic tree with clades collapsed

In shipunov: Miscellaneous Functions from Alexey Shipunov

Plot phylogenetic tree with clades collapsed

Description

Plot phylogenetic tree with clades collapsed into triangles or rectangles

Usage

Plot.phylocl(tree, cl, strict=TRUE, keep.mono=FALSE, what="triangles",
 col.ed="black", col.td="black", col.etr="transparent", col.ttr="transparent",
 col.pfl="lightgrey", col.pbr="black", lty.p=1, lwd.p=1, col.ct="black",
 ct.off=0, ct.fnt=1, cex=par("cex"), longer="0%", ...)

Arguments

tree	phylo object
cl	two columns classification table
strict	default TRUE: do not join all descendants
keep.mono	default FALSE: do not keep monotypic clades
what	default "triangles", also possible to use "rectangles"
col.ed	default "black", default edge color
col.td	default black", default tips color
col.etr	default "transparent", color to suppress original edges
col.ttr	default "transparent", color to suppress original tips
col.pfl	default "lightgrey", fill color for polygons
col.pbr	default "black", border color of polygons
lty.p	default 1, line type of polygon borders
lwd.p	default 1, line width
col.ct	default "black", color of clade labels
ct.off	default 0, text offset of clade labels
ct.fnt	default 1, text font of clade labels
cex	default par("cex"), text font size of all labels
longer	default "0%", percent to increase xlim to fit longer clade labels
...	options to ape::plot.phylo()

Details

Plot.phylocl() plots phylogenetic tree with clades collapsed into triangles or rectangles.

Alternative is phytools::plot.backbonePhylo() which however requires more manual work.

Some tricks used (null plotting and transparent elements), the last one is actually useful in other ways.

Intersections and other deviated cases not controlled. However, they are really easy to spot.

All parameters of polygons should be either "scalars" or vectors of the same length as clade list (minus monotypic clades), clades are in alphabetical order. To help, list of clade names is invisibly returned in the end.

If keep.mono=TRUE, then monotypic clades must have names in the clade list, otherwise this option is useless.

Value

Returns list of clade names.

Author(s)

Alexey Shipunov

See Also

phytools::plot.backbonePhylo()

Examples

aa.d <- hclust(dist(t(atmospheres)))
tree <- ape::unroot(ape::as.phylo(aa.d))

cl <- data.frame(
planet=c(
 "Mercury",
 "Venus",
 "Earth",
 "Mars",
 "Jupiter",
 "Saturn",
 "Uranus",
 "Neptune"),
clade=c(
 "Mercury",
 "Mars group",
 "Earth",
 "Mars group",
 "Close giants",
 "Close giants",
 "Distant giants",
 "Distant giants"),
stringsAsFactors=FALSE)

Plot.phylocl(tree, cl, longer="5%", ct.off=0.1)

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.