tag:blogger.com,1999:blog-8499895524521663926.post3826595689833604903..comments2024-03-08T04:19:23.697-05:00Comments on Phylogenetic Tools for Comparative Biology: Adding spaces between genus & specific names in tree objectsLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-8499895524521663926.post-45886672164997832962021-09-25T14:08:08.838-04:002021-09-25T14:08:08.838-04:00using plot. phylo command, tree size is bigger and...using plot. phylo command, tree size is bigger and some labels also get cut. how to reduce the size. is there anything like fan.size=0.5 ...zafarhttps://www.blogger.com/profile/02945155562923084739noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-76250713433845686052012-02-21T16:54:25.918-05:002012-02-21T16:54:25.918-05:00Sure thing, Liam!
http://cran.r-project.org/web/p...Sure thing, Liam!<br /><br />http://cran.r-project.org/web/packages/paleotree/index.html<br /><br />My package is paleotree and it is focused on offering useful functions for paleontological data, particularly when phylogenetic approaches are used in the fossil record. Although there are a number of functions with miscellaneous uses, it focuses on four things: (1) estimating sampling rates from taxonomic ranges in the fossil record, (2) simulating taxon ranges and converting ranges into a phylogeny, (3) time-scaling cladograms of fossil taxa and (4) plotting diversity curves from fossil data in a way that is comparable to lineage diversity curves from phylogenies.dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-49606738888240392652012-02-21T16:44:54.629-05:002012-02-21T16:44:54.629-05:00Yes, that sounds like a good idea. Maybe I will pu...Yes, that sounds like a good idea. Maybe I will put that into the next version of plotSimmap (and phytools).<br /><br />Why don't you post a link to your package so we can check it out.<br /><br />Thanks! LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-83224336366218930062012-02-21T16:25:18.509-05:002012-02-21T16:25:18.509-05:00Couldn't you just make the gsub() line interna...Couldn't you just make the gsub() line internal to plotTree, right before the actual plotting the labels takes place? It seems like, from a programming point of view, that might be the safest course of action as people would then not be at risk of changing their tree object just to plot it and then forgetting this later in an analytical procedure.<br /><br />(This of course assumes that no one, ever, would want to plot underscores in tip labels. I would bet cash against the possibility, though.)<br /><br />Either way, thanks for the tip! I had never played around with gsub() or any of the string manipulation functions much before.<br />-Dave B.<br /><br />PS: I have a library up on CRAN too now! :)dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-28889943248986074922012-02-21T12:40:05.521-05:002012-02-21T12:40:05.521-05:00Of course, we can also go back if we want to write...Of course, we can also go back if we want to write the tree to file:<br /><br />tree$tip.label<-gsub(" ","_",tree$tip.label)<br />write.tree(tree,file="treefile.tre") # or<br />write.simmap(tree,file="treefile.tre")Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.com