Plot tree differences

Source: R/plotTreeDiff.R

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.

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,
  ...
)

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

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.

See also

medTree, tipDiff

Author

Michelle Kendall michelle.louise.kendall@gmail.com

Examples

## 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)