Hi all.
I am newbie for R bioinformatics.
I want to show traits of each tip of phylogeny.
In adephylo, I thought the function of table.phylo4d was similar to what I wanted.
X<-phylo4d(rcoal(5),matrix(c(1,2,2,3,1,2,2,1,1,4,4,3,2,3,2),nrow=5))
X
label node ancestor edge.length node.type V1 V2
1 t5 1 9 0.06701851 tip 1 2
2 t2 2 9 0.06701851 tip 2 2
3 t3 3 8 0.13961146 tip 2 1
4 t1 4 8 0.13961146 tip 3 1
5 t4 5 7 0.33118901 tip 1 4
6 <na> 6 0 NA root NA NA
7 <na> 7 6 0.69863476 internal NA NA
8 <na> 8 7 0.19157755 internal NA NA
9 <na> 9 6 0.96280526 internal NA NA
V3
1 4
2 3
3 2
4 3
5 2
6 NA
7 NA
8 NA
9 NA
> table.phylo4d(X)
But the result was different what I had expected.
The extend of circles did not respond to number of traits.
For instance, I want to same color or same extent of circle for identical numbers of traits.
But the result showed random extent or color for each trait.
I think I misunderstood the function of "table.phylo4d".
Please let me know what I have to do to get what I want.
Thank you.