plotShits: plotShifts
In hferg/hfgr:

Description Usage Arguments

Plots the locations of the origins of scalars from the postprocessor output of bayestraits. CURRENTLY WORKS ONLY FOR DELTAS.

plotShifts(PP, scalar, threshold = 0, colour = "red", direction = FALSE,
  scaled = "time", cex = 1, tips = FALSE, edge.cols = "black",
  edge.width = 1, main = "", scale = TRUE, bordercol = "black",
  border.width = 1, measure = "median", excludeones = FALSE,
  relativetrans = FALSE, transparency = TRUE,
  gradientcols = c("dodgerblue", "firebrick1"))

`PP`	The psotprocessor (localscalrPP) output.
`scalar`	The scalar to find and plot from the post processor - delta/lambda/kappa/node/branch
`threshold`	Threshold of probability in posterior to display deltas for, defaults to zero (i.e. shows all deltas shaded proportionally to the posterior probability)
`colour`	The colour to use for the node circles
`direction`	If TRUE nodes are identified with an upward triangle if the parameter is > 1 and a downward if < 1
`scaled`	Plot the original tree (scaled = "time", the default), or the mean/sclaed tree (scaled = "mean") or plot the tree scaled only by scalars present above the threshold (scaled = "threshold")?
`cex`	The scaling factor for the size of the node circles
`tips`	Show tip labels?
`edge.cols`	A vector of edge colours for the phylogeny
`main`	Title for the plot
`scale`	Include scale bar?
`bordercol`	If using directional arrows, what colour is the border of the triangles?
`border.width`	Width of the border of the triangles if using direction.
`measure`	When plotting "siginficant" tree, what measure of the parameter? Median (default), mode or mean.
`relativetrans`	If TRUE (defaults to FALSE) the scale of transparency will go from the threshold (totally transparent) to the maximum presence (full opacity).
`transparency`	Plot the node labels according to their presnce in the posterior?
`gradientcols`	A vector of two colours - the min and max colours used when colouring the tree according to percentage time rate scaled (when threshold = 0)
`exludeones`	If plotting according to a threshold of significance, should 1s (i.e. no scalar) be excluded from the posterior when calculating average scalar?