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.

Hi Liam,

ReplyDeleteGreat function! Would it be a simple addition to allow error bars to be plotted over this plot so that the variance of the trait can be better visualized? Any advice would be appreciated.

Hi Jacob. If you update to current version of phytools on GitHub you can modify any arguments to barplot using args.barplot. You can also add features to the plot after plotting, such as error bars as you suggest. You may also be interested in the function plotTree.boxplot which plots a boxplot next to a tree in a similar way. - Liam

DeleteLiam, it´s possible to use apply some function like tiplabels() to display some categorical information about species? (as you show elsewhere http://lukejharmon.github.io/ilhabela/instruction/2015/07/03/ancestral-states-2/)

ReplyDeleteHi

ReplyDeleteI learn a lot of things from your post , thank you. I am wondering if you are an implemented code in to have a bar plot with two y variables (beside =T). I have two variables : genome size(Mb) and gene density(genes/Mb, the plot is not so meaningful if i get them in only one y axiz when I use your plotTree.barplot code

Something like this would probably help: http://blog.phytools.org/2017/10/plottreebarplot-with-multiple-stacked.html.

DeleteHi,

ReplyDeletethank you so much for your posts! I was wondering if it's possible to use stacked bars with plotTree.wBars?

Kind of - but you have to do it manually: http://blog.phytools.org/2018/04/update-hack-to-get-stacked-bars-in.html.

DeleteThis comment has been removed by the author.

ReplyDeleteHi Liam

ReplyDeleteFirstly, thank you for this website it is a great resource of tremendous help

When I try and create a stacked bar plot as above I receive the following error message

"Error in plot.window(xlim = xlim, slim = slim, asp = asp):

need finite 'slim' values"

Any help you can give regarding this error message will be greatly appreciated!

Edit: "Error in plot.window(xlim = xlim, ylim = ylim, asp = asp):

Deleteneed finite 'ylim' values"

Do you have the latest phytools version? If so, you could try sending me your R workspace & the commands producing the error and I could try to figure it out for you.

DeleteI'm sure this has been resolved, but I had a similar problem and wanted to share in case other folks came across this issue as well. I solved it by removing the spaces between the genus and species epithet in my dataset (changing "Genus species" to "Genus_species"). Hope that helps anyone else with a similar problem!

DeleteHi Liam,

ReplyDeleteHow do you change the position of the scale at the bottom of the graph and for 100% stacked bar graphs that take up the whole panel is it not possible to add a legend?

Hi Liam,

ReplyDeleteYour package phytools is really amazing! So far, I had no problem in plotting metadata associated to my phylogenetic trees, but I'am struggling to combine the results of a dottree and a plotTree.barplot on the same tree. I'm playing with margines and ylim or xlim but it is not straitforward. If you have a solution, I would gladly take it. Thank in advance.

JC

Hi Liam,

ReplyDeleteThank you for your wonderful tutorials! Have you seen a way to combine a barplot with a circular tree? Apologies if I have missed this.

Thanks in advance,