Line up tree node labeles

[AgustinPardo]

Hello,

I execute the next lines to get a figure:

library(phytools)
library(mapdata)
gps<-read.csv("/home/agustin/workspace/covid-19/mapeo_arbol/gps_data.dat",header=TRUE)
rownames(gps) <- gps$ID
nwk=read.newick("/home/agustin/workspace/covid-19/mapeo_arbol/arbol_id_root_10.nwk")

obj<-phylo.to.map(nwk,gps[1:179,2:3],fsize=0.4,lwd=0.5,pts=FALSE,
                  direction="rightwards",database="worldHires", 
                  regions=c('Brazil', 'Colombia', 'Uruguay', 'Chile', 'Argentina', 'Peru',"Falkland"), 
                  rotate=FALSE)

I get this figure:

Do you know how to line up the tree node labels as you made in you figures:

Regards

Agustin

[liamrevell]

Agustin. The function plots your input tree, so most likely your input tree does not have tips that line up. If you want them to line up, you need to input an ultrametric tree to the function. If the current edge lengths don't mean anything (it looks like they all have the same length) you could use the arbitrary branch lengths of compute.brlen in the ape package. For instance:

 obj<-phylo.to.map(compute.brlen(nwk),gps[1:179,2:3],fsize=0.4,lwd=0.5,pts=FALSE,
                  direction="rightwards",database="worldHires", 
                  regions=c('Brazil', 'Colombia', 'Uruguay', 'Chile', 'Argentina', 'Peru',"Falkland"), 
                  rotate=FALSE)

[AgustinPardo]

That works perfectly! Many thanks!