Hi Klaus (and others),
Ah, I see! The real bug then appears to be in collapse.singles, as it
does not reorder the ID numbers in $edge. Here's a quick function to
return the root ID:
getRootID<-function(tree){
uniqueNode<-unique(tree$edge[,1])
whichRoot<-sapply(uniqueNode,function(x)
Hi David,
I found the bug. Somehow ape assumes on the one hand that the root is
number of tips + 1.
On the other hand the root of an phylo object is the node which is in
tree$edge[,1], but not in tree$edge[,2],
this is the case even in an unrooted tree. This annoys me for a long time.
The root of
Hello all,
As those of you who directly manipulate the guts of phylo objects in
your code (or construct new phylo objects whole cloth from
un-phylo-like data structures) have probably experienced, it is
sometimes easy to create $edge matrices that aren't accepted by ape
functions (I often use plot
Brilliant, space=500 sorted that out.
Alex
On Fri, 2015-06-12 at 17:14 +0200, Emmanuel Paradis wrote:
> Hi Alex,
>
> Try to increase the space between the trees (see the example in
> ?rotateConstr).
>
> Cheers,
>
> Emmanuel
>
> Le 10/06/2015 15:52, Aleksey Jironkin a écrit :
> >
> > Hi,
>
Hi Alex,
Try to increase the space between the trees (see the example in
?rotateConstr).
Cheers,
Emmanuel
Le 10/06/2015 15:52, Aleksey Jironkin a écrit :
Hi,
I have been struggling to get the links drawing properly on largeish
cophyloplot. I got the diagonal links to work on sample comman
