[Phylobase-devl] Root node number should be one plus number of tips?
Sang Chul Choi
Choi at Biology.Rutgers.Edu
Sat Apr 12 23:17:33 CEST 2008
Hi,
Continued from the previous message, getLabelByNode() function behaves
not quite right. I think that trees seem to be handled assuming
somthing in phylobase package not exactly based on user's input of
tree structure matrix. In the example of tree1, node 1 is labelled
"T5" but it prints "T1," and node 8 is labelled "N2", but it prints
"N3." Root node 9 is is labelled "N1," and it prints error message.
Thank you,
Sang Chul
m <- rbind(c(6,8),c(8,7),c(9,6),c(6,5),c(8,4),c(9,3),c(7,2),c(7,1))
m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
0.32102756, 1.97222694, 0.27245865, 0.27245865)
tree1 <- phylo4(edge=m, edge.length=m.l)
rootNode(tree1)
print(tree1)
getLabelByNode(tree1, 1)
getLabelByNode(tree1, 8)
getLabelByNode(tree1, 9)
On Apr 12, 2008, at 4:37 PM, Sang Chul Choi wrote:
> Hi,
>
> In my previous message, the first tree's root is 9 but, using
> rootNode() function it returns 6, so it may returns one plus number of
> tips.
>
> Thank you,
>
> Sang Chul
>
> m <- rbind(c(6,8),c(8,7),c(9,6),c(6,5),c(8,4),c(9,3),c(7,2),c(7,1))
> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
> tree1 <- phylo4(edge=m, edge.length=m.l)
> rootNode(tree1)
>
> On Apr 11, 2008, at 12:56 PM, Sang Chul Choi wrote:
>> Hi,
>>
>> I made trees using phylo4 object with time. I tested if it is
>> ultrametric using is.ultrametric, and I also write it to a tree file.
>> It seems that the if root node number is not one plus number of tips,
>> then ultrametric and write.tree does not seem to work. Maybe there is
>> help document how to create a tree in APE or phylobase package, but I
>> could not see any requirement except that matrix first column is for
>> ancestors, and second column is for descendants.
>>
>> Is there any further requirement for making trees other than this
>> (that matrix first column is for ancestors, and second column is for
>> descendants)?
>>
>> I am trying to update trees or subtree pruning and regrafting kind of
>> work. I take edge information using edges() function and change it.
>> Using the changed edge matrix table, I recreate phylo4 object. This
>> would change root node numbers and changed trees are behave
>> "awkwardly" (I guess only) to me. By the way, I found a "nice"
>> function in APE, "reorder", which does somehow help me to change tree
>> internal information so that tree can properly manipulated by APE
>> function. Is there a function in phylobase that change tree internal
>> structure so that tree internal information is corrected?
>>
>> I do not think that this is a bug, but it is something that is not
>> that I expected.
>>
>> Thank you,
>>
>> Sang Chul
>>
>> Just if anybody is interested in (I guess not) what I am doing?
>> CODE start:
>> All trees are 5 tips binary ultrametric tree.
>> tree1: root number is 9 -> tree file has a tree with 4 tips, not
>> ultrametric
>> tree2: root number is 6 (6 and 9 are reversed from tree1) -> tree
>> file has the right tree
>> tree3: root number is 6, and change two internal node numbers (8 <-
>>> 9) -> tree file has the right tree.
>>
>> m <- rbind(c(6,8),c(8,7),c(9,6),c(6,5),c(8,4),c(9,3),c(7,2),c(7,1))
>> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
>> tree1 <- phylo4(edge=m, edge.length=m.l)
>> tree1 <- reorder(as(tree1, "phylo"))
>> print(tree1)
>> print(paste("Is tree1 ultametric?", is.ultrametric(tree1)))
>> print("Coal. Intervals")
>> print(coalescent.intervals(tree1)$interval.length)
>> write.tree(tree1, "1.tre")
>>
>> m <- rbind(c(9,8),c(8,7),c(6,9),c(9,5),c(8,4),c(6,3),c(7,2),c(7,1))
>> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
>> tree2 <- phylo4(edge=m, edge.length=m.l)
>> tree2 <- reorder(as(tree2, "phylo"))
>> print(tree2)
>> print(paste("Is tree2 ultametric?", is.ultrametric(tree2)))
>> print("Coal. Intervals")
>> print(coalescent.intervals(tree2)$interval.length)
>> write.tree(tree2, "2.tre")
>>
>> m <- rbind(c(8,9),c(9,7),c(6,8),c(8,5),c(9,4),c(6,3),c(7,2),c(7,1))
>> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
>> tree3 <- phylo4(edge=m, edge.length=m.l)
>> tree3 <- reorder(as(tree3, "phylo"))
>> print(tree3)
>> print(paste("Is tree3 ultametric?", is.ultrametric(tree3)))
>> print("Coal. Intervals")
>> print(coalescent.intervals(tree3)$interval.length)
>> write.tree(tree3, "3.tre")
>>
>> hylogenetic tree with 5 tips and 4 internal nodes.
>>
>> Tip labels:
>> [1] "T1" "T2" "T3" "T4" "T5"
>> Node labels:
>> [1] "N1" "N2" "N3" "N4"
>>
>> Rooted; includes branch lengths.
>> [1] "Is tree1 ultametric? FALSE"
>> [1] "Coal. Intervals"
>> [1] 0.46082282 1.32303995 0.04856891 0.13979526
>>
>> Phylogenetic tree with 5 tips and 4 internal nodes.
>>
>> Tip labels:
>> [1] "T1" "T2" "T3" "T4" "T5"
>> Node labels:
>> [1] "N1" "N2" "N3" "N4"
>>
>> Rooted; includes branch lengths.
>> [1] "Is tree2 ultametric? TRUE"
>> [1] "Coal. Intervals"
>> [1] 0.27245865 0.04856891 0.13979526 1.51140412
>>
>> Phylogenetic tree with 5 tips and 4 internal nodes.
>>
>> Tip labels:
>> [1] "T1" "T2" "T3" "T4" "T5"
>> Node labels:
>> [1] "N1" "N2" "N3" "N4"
>>
>> Rooted; includes branch lengths.
>> [1] "Is tree3 ultametric? TRUE"
>> [1] "Coal. Intervals"
>> [1] 0.27245865 0.04856891 0.13979526 1.51140412
>>
>>
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