Wrap-up & t-shirt design for Bariloche (Argentina) Macroevolution course

I just got back from teaching a five-day workshop the Universidad Nacional del Comahue in San Carlos de Bariloche, Argentina.

It was tiring, but a lot of fun - and I hope it was as rewarding for the students as it was for me.

As has become a tradition in the Latin American workshops that I teach (e.g., 1, 2, 3, 4, etc.), we have a course t-shirt - and, not only that, the t-shirt must be designed in R.

This year's workshop in Bariloche was not spared. Firstly, the design:

library(phytools)

## Loading required package: ape

## Loading required package: maps

library(plotrix)
source("http://www.phytools.org/Bariloche2016/data/arctext.R")
set.seed(545)
tree<-pbtree(n=78,scale=0.8)
txt<-write.tree(tree)
txt<-strsplit(txt,";")[[1]]
txt<-paste("((Y:0.9,",txt,":0.1):0.1,Z:1);",sep="")
tree<-read.tree(text=txt)
tree<-phytools:::lambdaTree(tree,0.95)
tree<-make.era.map(tree,c(0,0.4,0.8))
par(bg="darkgrey")
par(ljoin=1,lmitre=30)
par(mar=rep(0,4))
col<-rgb(red=117/255,green=170/255,blue=219/255)
par(fg="transparent")
plot(tree,colors=setNames(rep("black",3),1:3),
    lwd=10,type="fan",part=0.5,ftype="off",ylim=c(-0.2,1.2),
    lend=1)
par(fg="black")
plot(tree,colors=setNames(c(col,"white",col),1:3),
    lwd=8,type="fan",part=0.5,ftype="off",ylim=c(-0.2,1.2),
    lend=1,add=TRUE)
text(mean(par()$usr[1:2]),-0.15,"Bariloche, Argentina 2016",
    col="black",cex=2.7,font=2)
chars<-strsplit("Latin American Macroevolution Workshop","")[[1]]
stretch<-rep(1.1,length(chars))
arctext("Latin American Macroevolution Workshop",center=c(0,0),radius=1.1,
    cex=3.5,font=2,stretch=stretch)

(High resolution PDF with Times font for the text here.)

The only small wrinkle is that I tweaked the code of arctext in the plotrix package to get the text to look the way I wanted it to.

Finally, but most importantly, the students (& me) sporting our t-shirts:

(Click on image for larger version.)

Many thanks to course organizers Lina Moreno Azócar & Félix Cruz, who were wonderful hosts, helped put together a terrific course, and who also had the wonderful patience to drive me back & forth across the border to Chile (no small task) so I didn't have to fly through Buenos Aires!

Until next time Argentina!

Coloring tip nodes in phylomorphospace3d

I was just corresponding with a phytools user & essentially the lack of an argument node.col in the function phylomorphospace3d was broached.

Why this option doesn't exist, I couldn't tell you; however it is relatively easy to circumvent because the function invisibly returns a list of functions which can be used to plot points, lines, planes, etc., back in the original (simulated) space.

Here's a quick example, using simulated data:

library(phytools)
tree ## our tree

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

X ## our data

##          [,1]         [,2]        [,3]
## A -2.84172235  1.148037248  1.64782403
## B -2.05052328  1.431708869  1.15202298
## C -1.24686168  1.946696167  1.54897262
## D -0.52310503  0.573110584  0.46436125
## E -0.55578283  0.813448906  0.40254794
## F -0.51150759  1.733066759  1.49429840
## G  0.53936198  1.816801753  1.86050506
## H  0.01234429  2.302339855  2.63078614
## I -0.01684737  1.810997083  2.22857705
## J  1.32317051  2.492348110  0.55660832
## K  0.39032083  1.138053408 -0.42215854
## L  1.35224610  0.701773929 -0.73233992
## M  0.06642055  2.393143196  1.67769111
## N  0.53170462  2.387858206  1.07395647
## O  1.33893651  1.869361233  1.18002858
## P  0.16788769  1.722551818  0.03908209
## Q  0.72826260  0.591128118  1.23662094
## R  0.79698877  1.310841641  1.38182879
## S  0.08976056  1.727227579  2.10565084
## T  1.37506375 -0.551729936 -1.73123720
## U -1.09244120  0.960226117 -1.01694632
## V -0.75692309 -0.002878853 -1.02230472
## W -0.53535698 -0.168545803 -1.33846396
## X -0.26869690 -0.241183840 -1.14188545
## Y  0.19315024  0.282576551 -0.89620379
## Z -0.56460363 -0.613852876  0.98093216

y ## our character we want to map on the tips

##   A   B   C   D   E   F   G   H   I   J   K   L   M   N   O   P   Q   R 
## "c" "c" "b" "b" "b" "a" "a" "b" "b" "c" "c" "b" "c" "c" "c" "a" "c" "b" 
##   S   T   U   V   W   X   Y   Z 
## "b" "b" "c" "b" "c" "c" "c" "c"

tip.col<-y
tip.col[tip.col=="a"]<-"red"
tip.col[tip.col=="b"]<-"blue"
tip.col[tip.col=="c"]<-"yellow"
obj<-phylomorphospace3d(tree,X,method="static")
obj$points3d(X,cex=1.4,pch=21,bg=tip.col[rownames(X)])

That's it.

The tree & data were simulated as follows:

X<-fastBM(tree,nsim=3)
Q<-matrix(c(-1,1,0,1,-2,1,0,1,-1),3,3)
rownames(Q)<-colnames(Q)<-c("a","b","c")
y<-sim.history(tree,Q)$states

Custom color palettes in plotBranchbyTrait

I recently received the following user request:

“I have a small question regarding your phytools function plotBranchbyTrait that I was hoping you perhaps could help with. I am trying to visualize [my data with range 0 to 1] using the heat.color palette. However, as some species have a proportion of 0, and others have a proportion of 1, the branches leading to the latter are almost white and thus impossible to see. If I change the proportion of one of these species to, say 1.2, most of branches become more visible (except the branch leading to that particular species of course). However, this is not an ideal way to go about it. Is there any way I can make sure to only use parts of the color palette for the plot, excluding the brightest, white colors?”

Indeed, this effect can easily be verified using simulation:

library(phytools)
tree<-pbtree(n=100)
x<-fastBM(tree,scale=1)
plotBranchbyTrait(tree,x,"tips","heat.colors",show.tip.label=FALSE)

We can see that tips & edges with the most extreme values of the trait essentially vanish.

[Note that plotBranchbyTrait is unusual among phytools functions in that it uses ape::plot.phylo internally instead of plotSimmap in my package - hence the argument show.tip.label=FALSE which would be ftype="off" in most other phytools functions.]

The easiest way to address this was to allow the argument palette to be supplied as a function as well as as a string. I pushed this update to GitHub already & it can be seen here.

Here's an example:

plotBranchbyTrait(tree,x,"tips",
    palette=colorRampPalette(c("red","orange","yellow")),
    show.tip.label=FALSE)

We can even write our own custom function, for instance using the original heat.colors palette function internally, but cutting off the last (say) 5% of the spectrum:

foo<-function(n){
    obj<-heat.colors(round(1.05*n))
    obj[1:n]
}
plotBranchbyTrait(tree,x,"tips",palette=foo,show.tip.label=FALSE)

Finally, because plotBranchbyTrait uses plot.phylo internally, we can use any of the plot.phylo options, such as:

plotBranchbyTrait(tree,x,"tips",foo,type="fan",show.tip.label=FALSE,
    legend=1.8)

plotBranchbyTrait(tree,x,"tips",foo,type="unrooted",show.tip.label=FALSE,
    legend=1.8)

and so on.

To get this update you can install phytools from GitHub using the package 'devtools' as follows:

library(devtools)
install_github("liamrevell/phytools")