passing arguments to geom_point2 with mapply

Question

My objective is pass lists as arguments to the function geom_point2 using lapply or analogously mapply. In similar situations, I had success passing a list (or lists) to geom_cladelabel as in:

mapply(function (x,y,z,w,v,u,t,s) geom_cladelabel(node=x, label=y,
align=F, etc. # Where x y z etc are lists.

Problem is related to the use of aes inside geom_point2. (not in geom_cladelabel):

In the case of geom_point2, the node info is inside aes, and I could't do it. Normally I do not get any error message, but it does not work.

The objective is to make this example work, but using mapply instead of writting geom_point2 two times.

# source("https://bioconductor.org/biocLite.R")
# biocLite("ggtree")
library(ggtree)
library(ape)
#standard code
newstree<-rtree(10)
node1<-getMRCA(newstree,c(1,2))
node2<-getMRCA(newstree,c(3,4))
ggtree(newstree)+ 
geom_point2(aes(subset=(node ==node1) ), fill="black", size=3, shape=23)+
geom_point2(aes(subset=(node ==node2) ), fill="green", size=3, shape=23)

#desire to substitute the geom_point2 layers with mapply or lapply:
#lapply(c(node1,node2), function (x) geom_point2(aes(subset=(node=x)))))

It's easier to help you if you provide a [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input data so we can run and test the code. — MrFlick, Aug 03 '17 at 19:22

RaphiS · Accepted Answer · 2017-11-03T17:15:33.513

2

Here is a solution calling geom_point2 usig mapply:

library(ggtree)
ggtree(rtree(10)) + 
  mapply(function(x, y, z) 
    geom_point2(
      aes_string(subset=paste("node ==", x)), 
      fill=y, 
      size=10, 
      shape=z
    ), 
    x=c(11,12), 
    y=c("green", "firebrick"), 
    z=c(23,24)
  ) +
  geom_text2(aes(subset=!isTip, label=node))

The solution is in the aes_string(), which writes the value of x directly in the aesthetics. The default aes() does not pass on the value of x, but just the string "x". When plotting, ggtree then looks for a node called "x", and ends with an empty node list. I guess this has to do with the variable being stored in the mapply-environment and not being passed on to the plot.

PS: Sorry for my too quick answer with do.call() earlier. It is useful, but off-topic here.

edited Nov 03 '17 at 17:15

answered Nov 02 '17 at 19:44

RaphiS

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Please try to add some sort of explanation alongside answers. This may be great code offering the perfect solution, but without some explanation it lacks any supporting evidence and makes it hard for others to learn what is going on or even generally learn for future reference. – Phill Healey Nov 02 '17 at 20:43
1

Thanks @PhillHealey for pointing this out. First answer was a quick guess. Adjusted now, hope this fits better. – RaphiS Nov 03 '17 at 17:21

passing arguments to geom_point2 with mapply

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