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
.
1 2 3 |
tr1 |
an object of the class |
tr2 |
an object of the class |
tipDiff |
an optional input, the result of |
vec1 |
an optional input, the result of |
vec2 |
an optional input, the result of |
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 |
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 |
the method to use for colouring. Default is "ramp", corresponding to the original implementation, where the function |
palette |
the colour palette to be used if |
... |
further arguments passed to |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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)
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