tag:blogger.com,1999:blog-8499895524521663926.post3574093666938631938..comments2024-03-08T04:19:23.697-05:00Comments on Phylogenetic Tools for Comparative Biology: Specifying node colors with phylomorphospace()Liam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-8499895524521663926.post-80076935731924249922020-12-26T10:11:35.318-05:002020-12-26T10:11:35.318-05:00Amazing, thank you!!
Amazing, thank you!! <br />Stephanie Shttps://www.blogger.com/profile/04688720318016209621noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-45035836838725209592020-05-01T12:42:35.104-04:002020-05-01T12:42:35.104-04:00Is there a way to use open circles for the tips?
Is there a way to use open circles for the tips?<br />Guilhermehttps://www.blogger.com/profile/02354064052300012379noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-41580161612537757642013-05-26T17:38:32.707-04:002013-05-26T17:38:32.707-04:00Hi Liam,
that did the trick, thanks for the advice...Hi Liam,<br />that did the trick, thanks for the advice.<br />cheersAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-18185673475805934062013-05-23T20:31:58.763-04:002013-05-23T20:31:58.763-04:00I understand that the Windows binary has been buil...I understand that the Windows binary has been built & this will be available through CRAN within 25 hrs. or so. Thanks! LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-16802279389071380952013-05-23T20:09:27.572-04:002013-05-23T20:09:27.572-04:00Hi Liam,
I can't seem to find a newer Windows ...Hi Liam,<br />I can't seem to find a newer Windows version of phytools than 0.2-50. I'm sure this is the same issue someone identified a few weeks ago (somehow I missed it in the blog).Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-22293789577832122022013-05-23T06:03:59.379-04:002013-05-23T06:03:59.379-04:00Also - there is a newer CRAN version of phytools.Also - there is a newer CRAN <a href="http://blog.phytools.org/2013/05/new-version-of-phytools-on-cran.html" rel="nofollow">version of phytools</a>.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-76518601314151894232013-05-23T06:03:18.286-04:002013-05-23T06:03:18.286-04:00Hi. This is just because phytools dependency '...Hi. This is just because phytools dependency 'ape' and a dependency of 'phangorn' ('igraph') have conflicting function names. Basically unless you intend to use those function (as.igraph or edges) - don't worry about it. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-57611179650021198102013-05-23T05:37:47.224-04:002013-05-23T05:37:47.224-04:00Hi Liam,
I'm using phytools version 0.2-50 (fo...Hi Liam,<br />I'm using phytools version 0.2-50 (for Windows). I did notice when I load the phytools library file I get the following message:<br />'Loading required package: rgl<br />Warning messages:<br />1: replacing previous import ‘as.igraph’ when loading ‘igraph’ <br />2: replacing previous import ‘edges’ when loading ‘igraph’ '<br />Any suggestions appreciatedAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-72011557563141115102013-05-22T06:23:16.351-04:002013-05-22T06:23:16.351-04:00Can you post which version of phytools you are usi...Can you post which version of phytools you are using (check with packageVersion("phytools")). There is a known bug in the latest CRAN release (described <a href="http://blog.phytools.org/2013/05/bug-fix-update-to-phylomorphospace.html" rel="nofollow">here</a>), but I don't know of any problems (yet) in the most recent non-CRAN version (<a href="http://www.phytools.org/nonstatic/phytools_0.2-64.tar.gz" rel="nofollow">phytools 0.2-64</a>). Thanks!Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-37886135002910820232013-05-22T06:11:19.012-04:002013-05-22T06:11:19.012-04:00Hi Liam,
has this function been somehow changed to...Hi Liam,<br />has this function been somehow changed to any extent. I've just upgraded to the most recent version of phytools, and now when I attempt to specify node colors when plotting, I get no colored nodes on the plot (using the exact same script and data that worked previously)? No error messages or anything informative appear when this happens. Any insights appreciatedAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-70750560643647091072013-03-21T13:30:02.334-04:002013-03-21T13:30:02.334-04:00Terrific. Glad to hear it.Terrific. Glad to hear it.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-37599195768762470362013-03-21T12:46:11.063-04:002013-03-21T12:46:11.063-04:00Works perfect! I tried the phenogram with tidy lab...Works perfect! I tried the phenogram with tidy labels and also works perfect.<br />Thanks a lot! Conostegiahttps://www.blogger.com/profile/00182499478812939067noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-73288411074084309552013-03-21T11:40:05.548-04:002013-03-21T11:40:05.548-04:00Answered here. I hope this helps. LiamAnswered <a href="http://blog.phytools.org/2013/03/coloring-all-nodes-of-subtree-same.html" rel="nofollow">here</a>. I hope this helps. LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-80584255751344467162013-03-21T07:07:47.787-04:002013-03-21T07:07:47.787-04:00I did try reading in the list as you suggested abo...I did try reading in the list as you suggested above but had no success.Conostegiahttps://www.blogger.com/profile/00182499478812939067noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-58099760079465994022013-03-18T21:54:15.756-04:002013-03-18T21:54:15.756-04:00Hi Liam!
Is there a way to use getDescendents() t...Hi Liam!<br /><br />Is there a way to use getDescendents() to color the tips that descend from a certain node (including or excluding the node colors) to use in phylomorphospace()? And if there are several clades one would like to color, how to use the objects of getDescendents for the different clades in the same phylomorphospace?<br /><br />Thanks for any advice!<br />RicardoConostegiahttps://www.blogger.com/profile/00182499478812939067noreply@blogger.com