tag:blogger.com,1999:blog-1871542942842750523.post6052077277290454300..comments2023-07-24T10:40:57.739-04:00Comments on dechronization: R Tip: Indicating Tree SupportGlorhttp://www.blogger.com/profile/17707197225963721646noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-1871542942842750523.post-49981213859666251492008-08-02T09:48:00.000-04:002008-08-02T09:48:00.000-04:00Thanks man. It should be fixed now. I screwed up...Thanks man. It should be fixed now. I screwed up when revising my original into html format with appropriate tags for math symbols.Glorhttps://www.blogger.com/profile/17707197225963721646noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-72964907651272359012008-08-02T09:30:00.000-04:002008-08-02T09:30:00.000-04:00Hey Rich,thanks for the script! I think this line ...Hey Rich,<BR/><BR/>thanks for the script! I think this line should be changed to >= 0.95 or none of the high support nodes get labelled!<BR/><BR/>p[your_tree$node.label <= 0.95] <- "black"Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-4278147136263357272008-07-29T18:01:00.000-04:002008-07-29T18:01:00.000-04:00As long as node support numbers are explained in a...As long as node support numbers are explained in a little text box or in the legend (I prefer the former), shapes and colors are the way to go. R and <A HREF="http://ape.mpl.ird.fr" REL="nofollow">Ape</A>, specifically, are great for this purpose. Displaying the overall topology and magnifying interesting subtrees is the best move, to echo Susan. Rod Page among others has been working on interactive tree viewers.<BR/><BR/>Another way is to color internode branches in <A HREF="http://tree.bio.ed.ac.uk/software/figtree" REL="nofollow">FigTree</A>. One can specify not only colors, but the range of colors corresponding to a range of node support values as well as a line width range, so that internode branches leading to highly supported clades are thinker, and so on.sergios-orestis kolokotronishttps://www.blogger.com/profile/05492639186814501804noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-47686145566243384882008-07-27T10:10:00.000-04:002008-07-27T10:10:00.000-04:00I always say - the bane of systematics is that the...I always say - the bane of systematics is that the more data you collect, the more illegible your slide (or figure) is. It's always important to consider what you want your audience (or viewers) to take away. I've tended to favor the dots on nodes that are well supported - it is an immediate visual of a well-resolved tree - and then zoom in on clades of interest or be sure to discuss them so the point is clear. Not every node is (equally) interesting.Susan Perkinshttps://www.blogger.com/profile/05944116263349266952noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-13352162180297715042008-07-27T08:07:00.000-04:002008-07-27T08:07:00.000-04:00Any size is better than none, and in my own packag...Any size is better than none, and in my own package you get none in the graphic drawings of the trees. It is very hard to figure out how to put numbers on tiny little branches. Even symbols are a stop-gap measure and with enough, and small enough, branches that will fail too.<BR/><BR/>As an aside, you would not believe how many times I have gotten the complaint (for the tree-drawing programs Drawtree and Drawgram in PHYLIP) that the user is upset because they had the program draw their 800-tip tree on a single page <EM>and the species names were too small to read!</EM> I am mystified as to what else they expected to happen in that case. (I have options to draw the tree over multiple pages, but they don't even think of using that).Anonymousnoreply@blogger.com