plotTree.barplot with more user options, including stacked bars for multiple input traits

In response to a user comment I have added a feature to plotTree.barplot to permit multiple traits or values to be plotted for each species - either using stacked bars, or by plotting the bars side-by-side.

The update can be seen here. The problem turned out to be a little bit mroe complicated then it seemed it first, mainly because of a quirk in barplot that means that the object returned by boxplot (which I then use to correctly space the tips of the plotted tree) differs depending on whether the input data come in the form of a vector of single values or a matrix, &, if the latter, whether the argument beside=TRUE is selected or not.

Here's a quick & dirty demo. These data are (simulated to represent) relative frequencies - said dietary fraction of three different food types - so stacking of our bars is appropriate:

library(phytools)
packageVersion("phytools")

## [1] '0.5.70'

tree

## 
## Phylogenetic tree with 26 tips and 25 internal nodes.
## 
## Tip labels:
##  A, B, C, D, E, F, ...
## 
## Rooted; includes branch lengths.

X

##        plant  vertebrate invertebrate
## A 0.31086049 0.212175943   0.47696356
## B 0.15404215 0.440976975   0.40498087
## C 0.26982034 0.450834511   0.27934515
## D 0.12260206 0.358475976   0.51892197
## E 0.29979068 0.129743168   0.57046615
## F 0.20163877 0.440001107   0.35836012
## G 0.05465514 0.410528162   0.53481670
## H 0.47392116 0.121520364   0.40455848
## I 0.44344594 0.101251541   0.45530252
## J 0.24839375 0.268691107   0.48291514
## K 0.12309160 0.101699889   0.77520851
## L 0.24010676 0.065417274   0.69447597
## M 0.23424489 0.226431850   0.53932326
## N 0.40030662 0.057542453   0.54215092
## O 0.15332681 0.023255378   0.82341781
## P 0.44389924 0.491496743   0.06460401
## Q 0.27010640 0.292077796   0.43781581
## R 0.21643656 0.208244073   0.57531937
## S 0.19650159 0.317376110   0.48612230
## T 0.01261411 0.427646672   0.55973922
## U 0.32707264 0.164682573   0.50824478
## V 0.28931830 0.126987763   0.58369394
## W 0.08407750 0.252999348   0.66292315
## X 0.28631262 0.004105909   0.70958147
## Y 0.38118921 0.206806916   0.41200387
## Z 0.07941718 0.074216139   0.84636668

plotTree.barplot(tree,X)

Or, we can plot the bars side-by-side:

plotTree.barplot(tree,X,args.barplot=list(beside=TRUE,xlim=c(0,1),
    legend.text=TRUE,space=c(0,1.2),args.legend=list(x=1,y=17)))

Note that beside=FALSE is not a good option if our data have both positive & negative values as this can produce a weird result. For instance:

Y

##         [,1]        [,2]        [,3]
## A  0.7618018  2.59661203 -0.23590050
## B  0.8548063  1.40920654  0.73019040
## C -1.1970456  1.09259205  0.56974523
## D -0.4355176  2.31904920 -1.18347277
## E  2.2923226  2.35986558 -3.22201293
## F  2.5004466  3.98754763 -2.68168275
## G  2.7103706  1.94742983 -1.81626643
## H  1.4677625  1.90001387 -2.78720751
## I  1.5596683  4.57540030 -0.17596327
## J  1.5259543  5.22197986 -0.50073032
## K  1.4834068  4.99761663 -0.35070911
## L  1.3819468  4.84211948 -0.49581275
## M  1.4874512  4.99309837 -0.06583491
## N  0.3560632  3.50340705 -0.95027035
## O -0.2002478  3.80948866 -0.60808238
## P -0.9702761  3.93130784 -3.55745209
## Q -0.2638056  2.81862255 -2.47669725
## R  0.6922559  3.11378711 -3.53855007
## S -0.5630365  3.80538588 -2.87224419
## T  0.7185199  3.63159681 -0.96902150
## U  0.2464106  3.45631197 -0.05955653
## V -0.9173568  5.08132488 -3.08922774
## W -0.5006388  4.79906054 -3.26551534
## X  0.6836688  4.47601771 -3.28019095
## Y -0.5106440 -1.65927057 -0.89645983
## Z  0.3405579 -0.02014156 -0.76899774

plotTree.barplot(tree,Y)

If one is determined to use a barplot for these kind of data, I would recommend beside=TRUE which produces a more sensible result:

plotTree.barplot(tree,Y,args.barplot=list(beside=TRUE,space=c(0,1.2)))

That's it.