plotPhylogram.JM: Custom phytools:::plotPhylogram function to allow vertical...
In jacobmaugoust/ULT: Useful Little Things

plotPhylogram.JM

R Documentation

Custom phytools:::plotPhylogram function to allow vertical space between taxa of a horizontal phylogram

Description

Custom phytools:::plotPhylogram function to allow vertical space between taxa of a horizontal phylogram

Usage

plotPhylogram.JM(
  x,
  direction = "rightwards",
  x_gap = 0,
  ylim,
  y.label.offset,
  fsize = 0.75,
  ftype = "off",
  lwd = 4,
  pts = FALSE,
  node.numbers = FALSE,
  mar = rep(0, 4),
  add = FALSE,
  offset = 0,
  setEnv = TRUE,
  placement = "intermediate",
  tips = NULL,
  split.vertical = FALSE,
  lend = 2,
  asp = NA,
  plot = TRUE
)

Arguments

`x`	Mapping plot of phytools function (e.g., `plot.contMap`, `plotSimmap`) containing a phylogenetic `tree` and a vector of colors named `cols`
`direction`	Horizontal direction of the phylogram. Either `"rightwards"` or `"leftwards"`
`x_gap`	Numeric horizontal free space at the side of the plot, useful if one wants to contrast two trees. Default is 0
`ylim`	Classic `ylim` vector. Default is sum of number of tips and of vertical spaces between taxa
`y.label.offset`	Vector of same length than the number of tips of the tree. Needs to specify the offset of each tip (0 if same place, positive values otherwise).
`fsize`	Relative font size for tip labels.
`ftype`	Font type - options are `"reg"`, `"i"` (italics), `"b"` (bold), or `"bi"` (bold-italics)
`lwd`	Line width for plotting
`pts`	Logical value indicating whether or not to plot filled circles at each vertex of the tree, as well as at transition points between mapped states. Default is `FALSE`
`node.numbers`	Logical value indicating whether or not node numbers should be plotted. Default is `FALSE`
`mar`	Vector containing the margins for the plot to be passed to `par`. If not specified, the default margins all are 0
`add`	Logical value indicating whether or not to add the plotted tree to the current plot (`TRUE`) or create a new plot (`FALSE`, the default)
`offset`	Offset for the tip labels in character widths. Default is 0
`setEnv`	Logical value indicating whether or not to set the environment `.PlotPhyloEnv`. Setting this to `TRUE` (the default) will allow compatibility with ape labeling functions such as `nodelabels`
`placement`	Node placement following Felsenstein (2004; pp. 574-576). Can be `"intermediate"` (the default), `"centered"`, `"weighted"`, or `"inner"`
`tips`	Labeled vector containing the vertical position of tips. Normally this will be `1:N` for `N` tips in the tree.
`split.vertical`	Split the color of the vertically plotted edges by the state of the daughter edges. Only applies if the edge state changes exactly at a node
`lend`	Line end style. See `par`
`asp`	Aspect ratio. See `plot.window`
`plot`	Logical value indicating whether or not to actually plot the tree. (See equivalent argument in `plot.phylo`