I will be teaching a workshop at Universidad Austral de Chile in Valdivia in December. Right now I'm working on the design for the t-shirt that we have made a tradition in prior similar workshops (e.g., 1, 2).
I decided it might be cool to project a phylogeny onto the geographic outline of Chile. The only problem is that Chile is a very long country, and phylo.to.map previously only permits a projection of the tree from above facing down.
Well - that has now been addressed. I just pusheda phytools update that allows a phylogeny to be plotted to the left of a geographic map facing rightwards. Here is a demo.
First, we need to install from GitHub:
library(devtools)
install_github("liamrevell/phytools")
Load packages:
library(phytools)
library(phangorn) ## we will use phangorn too
For fun, let's use the lat. & long. coordinates of some major Chilean cities:
X<-read.csv("Chile-cities.csv",row.names=1)
X<-as.matrix(X)
X
## Lat Long
## Santiago -33.45 -70.67
## Valparaiso -33.05 -71.62
## Antofagasta -23.65 -70.40
## Temuco -38.75 -72.67
## Concepcion -36.82 -73.05
## Rancagua -34.17 -70.75
## Talca -35.43 -71.67
## Arica -18.48 -70.33
## Iquique -20.22 -70.15
## Puerto_Montt -41.47 -72.93
## La_Serena -29.90 -71.25
## Chillan -36.60 -72.12
## Osorno -40.57 -73.14
## Valdivia -39.75 -72.50
## Calama -22.47 -68.93
## Copiapo -27.36 -70.33
## Los_Angeles -37.47 -72.35
## Punta_Arenas -53.17 -70.93
(Hopefully I got most of these right!)
Rather than use a random “tree” - I figured why not compute a tree from the latitudinal distances between cities:
D<-dist(X[,1])
D
## Santiago Valparaiso Antofagasta Temuco Concepcion Rancagua
## Valparaiso 0.40
## Antofagasta 9.80 9.40
## Temuco 5.30 5.70 15.10
## Concepcion 3.37 3.77 13.17 1.93
## Rancagua 0.72 1.12 10.52 4.58 2.65
## Talca 1.98 2.38 11.78 3.32 1.39 1.26
## Arica 14.97 14.57 5.17 20.27 18.34 15.69
## Iquique 13.23 12.83 3.43 18.53 16.60 13.95
## Puerto_Montt 8.02 8.42 17.82 2.72 4.65 7.30
## La_Serena 3.55 3.15 6.25 8.85 6.92 4.27
## Chillan 3.15 3.55 12.95 2.15 0.22 2.43
## Osorno 7.12 7.52 16.92 1.82 3.75 6.40
## Valdivia 6.30 6.70 16.10 1.00 2.93 5.58
## Calama 10.98 10.58 1.18 16.28 14.35 11.70
## Copiapo 6.09 5.69 3.71 11.39 9.46 6.81
## Los_Angeles 4.02 4.42 13.82 1.28 0.65 3.30
## Punta_Arenas 19.72 20.12 29.52 14.42 16.35 19.00
## Talca Arica Iquique Puerto_Montt La_Serena Chillan Osorno
## Valparaiso
## Antofagasta
## Temuco
## Concepcion
## Rancagua
## Talca
## Arica 16.95
## Iquique 15.21 1.74
## Puerto_Montt 6.04 22.99 21.25
## La_Serena 5.53 11.42 9.68 11.57
## Chillan 1.17 18.12 16.38 4.87 6.70
## Osorno 5.14 22.09 20.35 0.90 10.67 3.97
## Valdivia 4.32 21.27 19.53 1.72 9.85 3.15 0.82
## Calama 12.96 3.99 2.25 19.00 7.43 14.13 18.10
## Copiapo 8.07 8.88 7.14 14.11 2.54 9.24 13.21
## Los_Angeles 2.04 18.99 17.25 4.00 7.57 0.87 3.10
## Punta_Arenas 17.74 34.69 32.95 11.70 23.27 16.57 12.60
## Valdivia Calama Copiapo Los_Angeles
## Valparaiso
## Antofagasta
## Temuco
## Concepcion
## Rancagua
## Talca
## Arica
## Iquique
## Puerto_Montt
## La_Serena
## Chillan
## Osorno
## Valdivia
## Calama 17.28
## Copiapo 12.39 4.89
## Los_Angeles 2.28 15.00 10.11
## Punta_Arenas 13.42 30.70 25.81 15.70
tree<-untangle(upgma(D),"read.tree") ## untangle is hack
(Use of untangle is a hack to ensure that the tree is in good conformation for phylo.to.map.)
Now let's proceed!
obj<-phylo.to.map(tree,X,regions="Chile",direction="rightwards",
plot=FALSE)
## objective: 32
## objective: 32
## objective: 32
## objective: 26
## objective: 26
## objective: 26
## objective: 8
## objective: 2
## objective: 2
## objective: 2
## objective: 2
## objective: 2
## objective: 2
## objective: 2
## objective: 2
## objective: 2
## objective: 0
obj
## Object of class "phylo.to.map" containing:
##
## (1) A phylogenetic tree with 18 tips and 17 internal nodes.
##
## (2) A geographic map with range:
## -55.89N, -17.51N
## -109.43W, -66.44W.
##
## (3) A table containing 18 geographic coordinates.
plot(obj,direction="rightwards",ftype="i")
One issue here is the spacing - which actually turns out to be the result of the inclusion in “Chile” of Chile's pacific island territories, such as Easter Island. Let's unceremoniously chop off those islands!
ii<-which(obj$map$x<(-77))
obj$map$x<-obj$map$x[-ii]
obj$map$y<-obj$map$y[-ii]
obj$map$range[1]<--81
plot(obj,direction="rightwards",split=c(0.6,0.4),ftype="i")
Finally, let's plot it with the tip labels removed & a special star at the location of our upcoming workshop!
plot(obj,direction="rightwards",split=c(0.3,0.7),ftype="off",
colors=c(grey(0.3),"black"))
points(X["Valdivia",2],X["Valdivia",1],pch=8,cex=1.2)
Not bad! Of course, as always, we can export a higher quality version using pdf:
pdf(file="phylo.to.map-Chile.pdf",width=5,height=8)
plot(obj,direction="rightwards",split=c(0.3,0.7),ftype="off",
colors=c(grey(0.3),"black"))
points(X["Valdivia",2],X["Valdivia",1],pch=8,cex=1.2)
dev.off()
## windows
## 2
Here it is!
That's all for now.