`plotTree`¶

Plot a tree

Description¶

Plot a tree

Usage¶

plotTree(tree, prune = NULL, keepSeqs = NULL, col = "black",
  leafCol = col, leafLabels = NULL, timeScale = 1, drawSpr = FALSE,
  sites = NULL, chromStart = NULL, chromEnd = NULL,
  ylab = "Generations", logScale = FALSE, ylim = NULL, add = FALSE,
  mar = c(8, 4, 1, 1), mod = NULL, cex.leafname = 0.8, ...)

Arguments¶

Argument	Description
`tree`	A newick string containing a tree
`prune`	A list of leafs to prune from the tree before plotting (Null means prune none)
`keepSeqs`	A list of leafs to keep in the tree (NULL means keep all)
`col`	Either a character string (single value) giving color of tree. Or, a list giving color to plot each leaf branch. Internal branches will be plotted as “average” color among child leafs.
`leafCol`	If given, this can be a list assigning a color to each leaf name (individual names also work if haploid names are in the form indName_1 and indName_2)
`leafLabels`	A list indexed by the leaf names in the tree, giving the label to display for each leaf name. If NULL, the leaf names are displayed.
`timeScale`	multiply all branches by this value
`drawSpr`	If TRUE, draw the SPR event that turns each tree into the next one
`sites`	If given, draw mutation events on tree
`chromStart`	The start coordinate of the tree region (1-based; only used if SITES not null)
`chromEnd`	The end coordinate of the tree region
`ylab`	label for y axis
`logScale`	If TRUE, plot in log scale
`ylim`	Range for y axis (default; use range of tree)
`add`	If TRUE, do not create a new plot
`mar`	Margins for plot
`mod`	(Advanced; for use with multi-population version of ARGweaver) A model file read in with the function readPopModel, will draw population model underneath tree
`cex.leafname`	Character size of leaf names
`...`	Passed to plot function

Note¶

This creates a new plot for each tree. If plotting to the screen, probably want to call par(ask=TRUE) first.