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.