tag:blogger.com,1999:blog-8499895524521663926.post848075722914708640..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: Convert a tree with a mapped character to a tree with singleton nodesLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-8499895524521663926.post-34965489803818961642015-07-06T17:13:44.405-04:002015-07-06T17:13:44.405-04:00Hello Liam,
Thanks for adding this functionality....Hello Liam,<br /><br />Thanks for adding this functionality. I trying to use the plotTree.singleton method in my scenario with the end goal of plotting ancestral state marginal probabilities as pie charts unto trees with singleton edges. To create these pie-charts, I'm using nodelabels and tiplabels functions (from ape). However, these functions don't seem to be supported on these singleton trees. Do you get errors if you try to call any of these two functions after calling plotTree.singletons in any of the above examples?<br /><br />In my scenario I'm running into unusual behaviour from the nodelabels function when I try to call these functions after plotting my tree with singletons edges. I can send a complete repro script with data and all, but a quick snippet of what I'm doing looks something like this:<br /><br />packageVersion("phytools")<br />[1] ‘0.4.56’<br />packageVersion("ape")<br />[1] ‘3.3’<br /><br />mt = read.newick(text="...")<br />plotTree.singletons(mt); #Looks good<br />nodelabels(); #No errors, but the labels are not overlapping the ancestral nodes<br />nodelabels(pie=marginals, piecol = cols); #ERROR<br />Error in pie[i, ] : subscript out of bounds<br /><br />Thanks for taking a look at this. Do let me know if plotting pie charts at the ancestral nodes for singleton trees are possible. Jaaved Mohammedhttps://www.blogger.com/profile/00263335839920858474noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-21793987349235704342013-09-22T16:15:38.173-04:002013-09-22T16:15:38.173-04:00Just to follow up, that was indeed true, but the C...Just to follow up, that was indeed true, but the CRAN version of ape was updated the day after this post, so the CRAN version (3.0.10) works fine now.Luke Mahlerhttps://www.blogger.com/profile/05074736091828507939noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-85738377249631323652013-09-09T22:28:50.633-04:002013-09-09T22:28:50.633-04:00Some reports from Luke suggest that this may depen...Some reports from Luke suggest that this may depend on the latest non-CRAN ape (download <a href="http://ape-package.ird.fr/" rel="nofollow">here</a>). I'm not going to roll back my version to check, but I will update if this is confirmed.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-67113878387561085382013-09-09T17:47:34.429-04:002013-09-09T17:47:34.429-04:00That shouldn't be too hard. If you have a spec...That shouldn't be too hard. If you have a specific example, then email me & I'll do it. LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-89144184152447522042013-09-09T16:51:31.724-04:002013-09-09T16:51:31.724-04:00Huh.
Have you considered the opposite, a function...Huh.<br /><br />Have you considered the opposite, a function that would convert a tree with singleton nodes and states for each edge, converted to a mapped character tree?<br /><br />I might have a use for such a thing... keeping track of ancestral taxa and ghost branches on a paleo-tree, for example.dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.com