plot.concor: Plot Concordances
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

Description Usage Arguments Details See Also

This function plot the ref tree with the percents or counts of concordances as node labels.

## S3 method for class 'concor'
plot(
  x,
  levelcol = NULL,
  thres = NULL,
  type = c("percent", "count"),
  node.cex = 0.5,
  node.adj = c(0.5, 0.5),
  node.frame = "rect",
  ...
)

`x`	an object from "`concor`".
`levelcol`	a character vector specifying the colors for node labels showing different levels of concordances. Defaults as `NULL`.
`thres`	a numeric vector specifying the levels for node labels to be plotted with different colors. Must be consistent with `type`. Defaults as `NULL`.
`type`	a character specifying the type of node labels. Can be either "percent" or "count".
`node.cex`	a numeric specifying the scale of node labels. Defaults to `0.5`.
`node.adj`	a numeric vector specifying the position of node labels. Defaults to `c(0.5, 0.5)`. Also see `plot.phylo`.
`node.frame`	a character specifying the type of frame of node labels. Must be one of "rect", "circle", "none", or unambiguous abbreviation. Also see `plot.phylo`. Defaults to "`rect`".
`...`	other arguments to be passed to `plot` or to `plot.phylo`.

thres is required with levelcol arg. On the other hand, levelcol can left as default when thres is set, then brewer.pal (in RColorBrewer pcakage) will be called to produce levelcol. Length of thres must be one more than levelcol.

concor.node, plot.phylo

Chien-Hsun/rePhylo documentation built on May 19, 2020, 3:15 a.m.