Re: [R-sig-phylo] multipage pdf of a huge tree

Mind=Blown. Amazing. Thank you. Jake On Mar 5, 2015, at 2:55 PM, Liam J. Revell liam.rev...@umb.edu wrote: Hi Jacob. This is surprising easy. Check out the solution here: http://blog.phytools.org/2015/03/splitting-tree-across-multiple-pages.html. You may find that, as in this

Re: [R-sig-phylo] multipage pdf of a huge tree

Hi Jacob. This is surprising easy. Check out the solution here: http://blog.phytools.org/2015/03/splitting-tree-across-multiple-pages.html. You may find that, as in this example, some things like node edge labels are split across pages - in which case you can fiddle with the split

Re: [R-sig-phylo] multipage pdf of a huge tree

OK - Actually I spoke too soon. That does work for nodelabels() and axis(), but it does not work for the axisGeo function in phyloch - this only appears at the bottom of the second half of the split plot when I split my tree in 1/2. Is there an easy fix to get it to appear on both 1/2s?

[R-sig-phylo] Node Ages Without Phylocom

Dear friends, I am trying to assign node ages to a phylogenetic tree of subtropical trees in southern Brazil without using Phylocom and its popular function bladj. This is because for some reason Phylocom will not open my Phylomatic-generated tree. I managed to open it with the rncl package as

Re: [R-sig-phylo] multipage pdf of a huge tree

Hi Liam, perfect! Your right, I didn't realize that some species were duplicated. Great to have the option in phytools! All the best, Jonas 2015-03-05 17:16 GMT+01:00 Liam J. Revell liam.rev...@umb.edu: Hi Jonas. I thought of the same thing. Unfortunately, one thing that I discovered is

Re: [R-sig-phylo] multipage pdf of a huge tree

Hi Liam, thanks a lot! I didn't knew splitplotTree yet. Great function! However, my tree has several thousands of tips (yes, it's a bit crazy but unfortunately necessary...) and I guess it's only possible to split it on two pages with splitplotTree. Or am I missing something? Thanks again! All

Re: [R-sig-phylo] multipage pdf of a huge tree

Hi Jonas. I thought of the same thing. Unfortunately, one thing that I discovered is that because R automatically adds 4% or so to the plotting range, you will find that species edges near the bottom of one page will also appear at the top of the next page. If you test your code look for

Re: [R-sig-phylo] multipage pdf of a huge tree

Jonas Eberle wrote: thanks a lot! I didn't knew splitplotTree yet. Great function! However, my tree has several thousands of tips (yes, it's a bit crazy but unfortunately necessary...) and I guess it's only possible to split it on two pages with splitplotTree. Or am I missing something?

Re: [R-sig-phylo] Stuck with Phylomatic tree!

Dear Alexandre, Your tree have some issues. One is the comments delimited by '[' and ']' at the end. You need first to remove those. Your tree ends like this: ... gymnosperms)seedplants,alsophila_sp)alsophila)cyatheaceae)))cyatheales)))monilophyte)euphyllophyte[NOTE: 4 taxa

Re: [R-sig-phylo] multipage pdf of a huge tree

Jonas Eberle -- thank you for your answer! Actually, I used to make large size pdfs with a tiny font size in these cases. It is then even possible to print this single-page-pdf on multiple pages in Acrobat Reader. The problem was that my current tree is really huge - with about 23000 tips.

Re: [R-sig-phylo] multipage pdf of a huge tree

Dear Joe, thank you for your answer! Actually, I used to make large size pdfs with a tiny font size in these cases. It is then even possible to print this single-page-pdf on multiple pages in Acrobat Reader. The problem was that my current tree is really huge - with about 23000 tips. This took me

Re: [R-sig-phylo] multipage pdf of a huge tree

One way to print a tree on multiple pages: In R, use the pdf() function and set the height of the page to be very large (say 110 inches if you want to print your tree on ten pages). Print the tree to the pdf file. Call dev.off() to close the pdf file. Then, when you print the tree with