plotTreeDiff: Plot tree differences
In treescape: Statistical Exploration of Landscapes of Phylogenetic Trees

Description Usage Arguments Value Author(s) See Also Examples

Highlight the topologicial differences between two trees, plotted side by side. This function is useful for comparing representative "median" trees - see medTree. It relies on the function tipDiff.

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plotTreeDiff(tr1, tr2, tipDiff = NULL, vec1 = NULL, vec2 = NULL,
  baseCol = "grey", col1 = "peachpuff", col2 = "red2",
  colourMethod = "ramp", palette = lightseasun, ...)

`tr1`	an object of the class `phylo`: the first tree to plot.
`tr2`	an object of the class `phylo`: the second tree to plot.
`tipDiff`	an optional input, the result of `tipDiff`. Supplying this will save time if calling `plotTreeDiff` repeatedly, for example with different aesthetics.
`vec1`	an optional input, the result of `treeVec(tr1, lambda=0)`. This argument is ignored if `tipDiff` is supplied; otherwise supplying this will save time if calling `plotTreeDiff` repeatedly, for example with different aesthetics.
`vec2`	an optional input, the result of `treeVec(tr2, lambda=0)`. This argument is ignored if `tipDiff` is supplied; otherwise supplying this will save time if calling `plotTreeDiff` repeatedly, for example with different aesthetics.
`baseCol`	the colour used for tips with identical ancestry in the two trees. Defaults to "grey".
`col1`	the first colour used to define the colour spectrum for tips with differences. This colour will be used for tips with minor differences. Defaults to "peachpuff". Ignored if `colourMethod="palette"`.
`col2`	the second colour used to define the colour spectrum for tips with differences. This colour will be used for tips with major differences. Defaults to "red2". Ignored if `colourMethod="palette"`.
`colourMethod`	the method to use for colouring. Default is "ramp", corresponding to the original implementation, where the function `colorRampPalette` is used to create a palette which ranges from `col1` to `col2`. For large trees this can be hard to interpret, and method `palette` may be preferred, which permits the selection of a palette to use in `adegenet`'s function `num2col`.
`palette`	the colour palette to be used if `colourMethod="palette"`. For a list of available palettes see `?num2col`.
`...`	further arguments passed to `plot.phylo`

A plot of the two trees side by side. Tips are coloured in the following way:

if each ancestor of a tip in tree 1 occurs in tree 2 with the same partition of tip descendants, then the tip is coloured grey (or supplied "baseCol")
if not, the tip gets coloured pale orange to red on a scale according to how many differences there are amongst its most recent common ancestors with other tips. The colour spectrum can be changed according to preference.

Michelle Kendall michelle.louise.kendall@gmail.com

medTree, tipDiff

## simple example on trees with five tips:
tr1 <- read.tree(text="((A:1,B:1):1,((C:1,D:1):1,E:1):1):1;")
tr2 <- read.tree(text="((A:1,B:1):1,(C:1,(D:1,E:1):1):1):1;")
plotTreeDiff(tr1,tr2)

## example on larger woodmice trees
data(woodmiceTrees)
# find the tip differences in advance, to avoid recalculating with each plot
wmTipDiff <- tipDiff(woodmiceTrees[[1]],woodmiceTrees[[2]])
plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff)
## change aesthetics:
plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff,
   baseCol="grey2", col1="cyan", col2="navy", 
   edge.width=2, type="radial", cex=0.5, font=2)
## use colour palette from adegenet:
plotTreeDiff(woodmiceTrees[[1]],woodmiceTrees[[2]], tipDiff=wmTipDiff,
   baseCol="black", colourMethod="palette", 
   edge.width=2, type="cladogram", cex=0.5, font=2)