Small update to default arguments of reroot

I just updated the phytools function reroot so that the default position along the edge at which to re-root the tree is at the node.number node supplied by the user. Previously, the function would not run when position was not supplied.

E.g.:

library(phytools)
plotTree(tree,offset=0.8)
nodelabels()
tiplabels()

Now, let's perform operations on this original tree:

## reroot 0.1 along edge leading to node 22
t_22<-reroot(tree,node.number=22,position=0.1)
plotTree(t_22)

## reroot halfway along edge leading to tip "D"
node<-which(tree$tip.label=="D")
position<-0.5*tree$edge.length[which(tree$edge[,2]==node)]
t_D<-reroot(tree,node,position)
plotTree(t_D)

## reroot at node 16
t_16<-reroot(tree,16)
plotTree(t_16)

## reroot at tip "A"
plotTree(t_A<-reroot(tree,which(tree$tip.label=="A")))

Note that in this function the argument position is the distance from the rootward end of the edge leading to node node.number at which the tree should be re-rooted. Also, though it is hard to demonstrate here, the function now has an interactive=TRUE mode (described here).

Refresher on plotting facing "contMap" objects, and some updates to plot methods

I received a question recently about how to plot two facing contMap style trees. I'm pretty sure I've covered this before, but here's a quick refresher.

## load phytools
library(phytools)
packageVersion("phytools")

## [1] '0.5.17'

## here are my tree & data
tree

## 
## Phylogenetic tree with 26 tips and 25 internal nodes.
## 
## Tip labels:
##  Z.hfundlvmi, Y.doctjxp, X.caqbgvj, W.ubmqztfgw, V.aitxenbrcp, U.vzfxlw, ...
## 
## Rooted; includes branch lengths.

X

##                  Trait 1   Trait 2
## Z.hfundlvmi   2.92865937  2.184148
## Y.doctjxp     2.06631025  2.286198
## X.caqbgvj    -2.94735743 -3.818020
## W.ubmqztfgw  -0.73396217 -1.942123
## V.aitxenbrcp  0.26393810 -2.086957
## U.vzfxlw      0.25402396 -2.109128
## T.prbgcsy     0.16793804 -1.725199
## S.wctpqhaf    0.35749291 -1.392195
## R.yxzaron    -4.87172318 -8.161849
## Q.qbxlo      -4.90003166 -7.796955
## P.ifcd       -4.37436361 -6.676666
## O.iojrpvxau  -0.84578913 -3.085084
## N.ytdhlvxrqz  1.17336030 -1.695673
## M.xfync       0.52891770 -1.657742
## L.zgbyowmia  -0.41660675 -2.401744
## K.mulpvq      0.06040434 -3.719370
## J.lnaxm      -0.12707579 -2.148399
## I.qfzjn      -5.45744073 -6.189724
## H.txlpg      -1.06821601 -2.431826
## G.xjzdfmubo  -2.50951467 -3.482821
## F.femtyazr   -6.16411522 -5.756618
## E.gowhzxfpb  -6.04269227 -6.048308
## D.pulivtfk    6.42009980  4.654686
## C.raopfz      2.79829549  3.821099
## B.mjuncdxt    4.48219431  5.865553
## A.ejysdxkti   4.10171985  5.524872

## create a layout for the trees & labels
layout(matrix(1:3,1,3),widths=c(0.4,0.2,0.4))
par(cex=1) ## make sure the correct font size is used in subplots
map1<-contMap(tree,X[,1],plot=FALSE) ## create "contMap" object
map1<-setMap(map1,invert=TRUE) ## invert color map
## plot "contMap" object
plot(map1,fsize=c(0,0.8),ftype=c("off","reg"),sig=1,legend=5,
    xlim=c(-0.1,1)*max(nodeHeights(tree)),mar=c(1.1,0.1,4.1,0.1))
title(main=colnames(X)[1])
## plot labels
ylim<-c(1-0.12*(length(tree$tip.label)-1),length(tree$tip.label))
plot.new()
plot.window(xlim=c(-0.1,0.1),ylim=ylim)
text(rep(0,length(tree$tip.label)), 1:length(tree$tip.label),tree$tip.label,
    font=3)
## repeat for trait 2
map2<-contMap(tree,X[,2],plot=FALSE)
map2<-setMap(map2,invert=TRUE)
plot(map2,fsize=c(0,0.8),ftype=c("off","reg"),
    direction="leftwards", sig=1,legend=5,
    xlim=c(-0.1,1)*max(nodeHeights(tree)),mar=c(1.1,0.1,4.1,0.1))
title(main=colnames(X)[2])

I added some new updates to phytools to permit this plotting.

1) I added user control of xlim in plot.contMap (and plot.densityMap). This is because I discovered that the legend was often being cut off for small plotting windows when xlim was set at its default values; and

2) I added the argument "direction" to add.color.bar which is used by plot.densityMap and plot.contMap internally to plot the legend. This has the effect of 'flipping' the direction of the color bar for left-facing trees which previously would have also been left-facing. (I don't think I noticed before.)

These data were simulated, obviously. The following gives the code I used for simulation:

## simulate a tree & make realistic looking tip labels
tip.label<-sapply(LETTERS[26:1],function(x) paste(x,".",
    paste(sample(letters,round(runif(n=1,min=4,max=10))),collapse=""),
    sep=""))
tree<-pbtree(n=26,tip.label=tip.label,scale=10)
## simulate correlated trait data
V<-matrix(c(1,0.8,0.8,1),2,2)
X<-sim.corrs(tree,V)
colnames(X)<-paste("Trait",1:2)

Note that there are other functions now available to visualize multiple continuous characters on a tree, such as phylo.heatmap:

phylo.heatmap(tree,X,fsize=c(1,1,0.8))

(although it doesn't look great for just two traits), or dotTree (which does):

dotTree(tree,X)

## or
dotTree(tree,X,standardize=TRUE)