fillClades: Highlight Clades in a Phylogeny
In heibl/viper: VIsualitaion of Phylogenetics and Evolution with R

Highlights one or more monophyletic groups (clades) in a phylogeny by filling them with color.

1	fillClades(phy, nodes, col, text, text.cex = 1, open.angle = 0)

`phy`	An object of class `phylo`.
`nodes`	A vector of mode `"numeric"` giving the most recent common ancestor (MRCA) node of the clades to be highlighted. You can use `noi` to obtain this vector.
`col`	A vector of mode `"character"` giving the color(s) of the clades; will be receycled if appropriate; default is `"grey"`.
`text`	A vector of mode `"character"`, giving (optional) text labels for clades; must be of the same length as `nodes`. The labels will be positioned right justified and vertically centered.
`text.cex`	Numeric, giving the character expansion (size) of the text labels.
`open.angle`	Numeric, giving the the angle left blank in degrees and has to match the value used in `plot.phylo` when choosing a circular plot type (`"fan"` or `"radial"`); for other plot types this has no effect.

On 2018-01-17, I added the optional plotting of labels. To this end, in non-ultrametric trees the tip-ward side of the polygons has to be aligned. This has only been tested for rightward phylograms. Maybe boxes should be extended vertically a bit to include tiplabels.And maybe the code should be organized a bit more systematically.

heibl/viper documentation built on May 21, 2019, 10:47 a.m.