plotPhylogram.JM: Custom phytools:::plotPhylogram function to allow vertical...

In jacobmaugoust/ULT: Useful Little Things

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

Details

See plotSimmap help page for more details

jacobmaugoust/ULT documentation built on May 16, 2023, 1:29 p.m.