plotTreeDiff: Plot tree differences

Description

Highlight the topological 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.

Usage

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

Value

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.

Arguments

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.
sizeOfDifferences: a logical (default FALSE) specifying whether the size of the tip differences should be used, or just a count of the number of differences (see tipDiff)
tipMatch: a logical (default TRUE) specifying whether the second tree should be rotated so that, as far as possible, each of its tips lies opposite its equivalent in the first tree
treesFacing: a logical (default FALSE) specifying whether the trees should be plotted facing each other - that is, with the second tree plotted "leftwards".
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

Author

Michelle Kendall michelle.louise.kendall@gmail.com

Examples

Run this code

## 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)
tr1 <- woodmiceTrees[[1]]
tr2 <- woodmiceTrees[[57]] # for example

# find the tip differences in advance, to avoid recalculating with each plot
wmTipDiff <- tipDiff(tr1,tr2, sizeOfDifferences=TRUE)
plotTreeDiff(tr1,tr2, tipDiff=wmTipDiff, tipMatch=TRUE)

## change aesthetics:
# trees facing each other:
plotTreeDiff(tr1,tr2, tipDiff=wmTipDiff, treesFacing=TRUE)

# radial plots, and change colours:
plotTreeDiff(tr1,tr2, tipDiff=wmTipDiff,
   baseCol="grey2", col1="cyan", col2="navy", 
   edge.width=2, type="radial", cex=0.5, font=2)
# cladogram plots, and use colour palette from adegenet to see differences more clearly:
plotTreeDiff(tr1,tr2, tipDiff=wmTipDiff,
   treesFacing=TRUE, baseCol="black", colourMethod="palette", 
   edge.width=2, type="cladogram", cex=0.5, font=2)    

# including the size of the differences highlights tip "No0906s" a little more:
# (this is typically a more informative plot in cases where many tips have the 
# same difference count, for example when a whole clade has been shifted "up" 
# or "down" the tree but its internal topology remains the same.) 
 
plotTreeDiff(tr1,tr2, tipDiff=wmTipDiff, sizeOfDifferences=TRUE,
   treesFacing=TRUE, baseCol="black", colourMethod="palette", 
   edge.width=2, type="cladogram", cex=0.5, font=2)