Tuesday, April 30, 2013

Showing posterior probabilities from describe.simmap at the nodes of a plotted tree

A user comment asks the following:

"I wonder how can I alter the size of the "pie" in describe.simmap.... Same question for altering the color...."

Well, there is no way at present to change the color or pie-size in describe.simmap(...,plot=TRUE); however, describe.simmap, it is easy to recreate the posterior probability plot of describe.simmap using the function output - while customizing its attributes.

Here's a quick demo:

> # check package version
> packageVersion("phytools")
[1] ‘0.2.54’
> # first simulate some data to use in the demo
> Q<-matrix(c(-2,1,1,1,-2,1,1,1,-2),3,3)
> rownames(Q)<-colnames(Q)<-letters[1:3]
> tree<-sim.history(pbtree(n=50,scale=1),Q)
> x<-tree$states
> # now the demo
> mtrees<-make.simmap(tree,x,model="ER",nsim=100)
make.simmap is sampling character histories conditioned on the transition matrix
Q =
          a        b        c
a -2.041867  1.020934  1.020934
b  1.020934 -2.041867  1.020934
c  1.020934  1.020934 -2.041867
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
        a        b        c
0.3333333 0.3333333 0.3333333
> XX<-describe.simmap(mtrees,plot=FALSE)
100 trees with a mapped discrete character with states:
a, b, c

trees have 23.93 changes between states on average

changes are of the following types:
      a,b  a,c  b,a  b,c  c,a  c,b
x->y 2.11 2.91 4.62 5.77 4.94 3.58

mean total time spent in each state is:
            a        b        c    total
raw  2.2816521 4.1930936 4.2593925 10.73414
prop 0.2125603 0.3906316 0.3968081  1.00000

> hh<-max(nodeHeights(tree))*0.02 # for label offset
> plot(tree,no.margin=TRUE,label.offset=hh,edge.width=2)
> nodelabels(pie=XX$ace,piecol=c("blue","red","green"), cex=0.5)
> tiplabels(pie=to.matrix(x,colnames(XX$ace)), piecol=c("blue","red","green"),cex=0.5)

Obviously, to adjust the pie-sizes & colors we just change the values of cex & piecol.

That's it.


  1. Great post! Very useful for plus-100-tips trees.

  2. Hi, I have problems with executing describe.simmap function.
    I have an object with phylogenetic trees with mapped discrete characters, but I have a problem like this:

    > simPP
    500 phylogenetic trees with mapped discrete characters

    Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
    'x' must be atomic

    Can you help me please?
    Thank you,

    1. Can you report your package version number & how the stochastic mapped trees were obtained (i.e., did they read from file or were they generated by make.simmap)?