Hi Jonas,I am still curious, why you are trying to print your tree. For me the best useful praxis to look at huge (not as huge as yours) phylogenies is with an svg file --> this is viewable (and scalable) in any Webbrowser and you can manipulate easily with inkscape. To export it just use 'RSvgDevice' or 'cairoDevice'.
Best Eike Mayland-Quellhorst -- __________________________________ Eike Mayland-Quellhorst AG Biodiversität und Evolution der Pflanzen Fakultät V - IBU Carl von Ossietzky Universität Oldenburg Carl-von-Ossietzky Str. 9-11 26111 Oldenburg Germany Tel. 0049-441-798-3386 Am 06.03.2015 um 12:00 schrieb r-sig-phylo-requ...@r-project.org:
Send R-sig-phylo mailing list submissions to
r-sig-phylo@r-project.org
To subscribe or unsubscribe via the World Wide Web, visit
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
or, via email, send a message with subject or body 'help' to
r-sig-phylo-requ...@r-project.org
You can reach the person managing the list at
r-sig-phylo-ow...@r-project.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-sig-phylo digest..."
Today's Topics:
1. Re: multipage pdf of a huge tree (Joe Felsenstein)
2. Re: multipage pdf of a huge tree (Jonas Eberle)
3. Re: multipage pdf of a huge tree (Joe Felsenstein)
4. Re: multipage pdf of a huge tree (Bret Larget)
5. Re: Stuck with Phylomatic tree! (Alexandre F. Souza)
6. Re: multipage pdf of a huge tree (Liam J. Revell)
7. Re: multipage pdf of a huge tree (Jonas Eberle)
8. Re: multipage pdf of a huge tree (Jacob Berv)
9. Re: multipage pdf of a huge tree (Liam J. Revell)
10. Re: multipage pdf of a huge tree (Jacob Berv)
11. Re: multipage pdf of a huge tree (Jacob Berv)
12. Node Ages Without Phylocom (Alexandre F. Souza)
13. determine multistate characters in nexus data matrix (Paolo Piras)
14. Re: Node Ages Without Phylocom (Marcelino de la Cruz)
----------------------------------------------------------------------
Message: 1
Date: Thu, 5 Mar 2015 03:41:38 -0800
From: Joe Felsenstein <j...@gs.washington.edu>
To: Jonas Eberle <eberle.jo...@gmail.com>
Cc: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] multipage pdf of a huge tree
Message-ID:
<cabxfcpej_qkq+3vwp_axfjnz9caxw9wxx67j7yde6j5u9vw...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
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?
>
It's not in R (unless available through Liam Revell's "phytools" package),
but in PHYLIP the tree-drawing programs Drawgram and Drawtree have the
capability of splitting a plot into a rectangular array of plots, and
putting these out onto separate files (not PDFs, but Postscript is
possible).
This was intended to help people make large posters using printers
that can
only do a single page.
However ...
I do not see why this is necessary. Most tree-drawing programs should be
able to write a file that has the large tree plotted on it. If you don't
want to print the resulting tree on paper, it would then be possible to
view the tree in an application such as Adobe Acrobat Reader and zoom
in on
it and see the tiny branches and their labels. Making multiple plots for
one tree would probably confuse the matter.
Or is there something I am missing here?
J.F.
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
[[alternative HTML version deleted]]
------------------------------
Message: 2
Date: Thu, 5 Mar 2015 13:24:35 +0100
From: Jonas Eberle <eberle.jo...@gmail.com>
To: Joe Felsenstein <j...@gs.washington.edu>
Cc: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] multipage pdf of a huge tree
Message-ID:
<CAJmKKNk9h=N4kPWVj=3ivWFZEae_R7NgKBqE7LA5J=bym3w...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
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
to the
limits of this approach, since pdf size is limited to 200 inch by
Adobe and
there also seems to be a lower limit for font size in pdfs (at least
during
export form R?).
I didn't knew that Drawtree is able to split the tree over multiple pages.
I guess this is an option in the command line version? I will check that
out. In the mean time I found a way to do the job in R (see my post
before)
that seems to produce reasonable results.
Thank you very much again for your efforts!
Regards,
Jonas
--
Jonas Eberle
PhD student
2015-03-05 12:41 GMT+01:00 Joe Felsenstein <j...@gs.washington.edu>:
>
> 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?
>>
>
> It's not in R (unless available through Liam Revell's "phytools"
package),
> but in PHYLIP the tree-drawing programs Drawgram and Drawtree have the
> capability of splitting a plot into a rectangular array of plots, and
> putting these out onto separate files (not PDFs, but Postscript is
> possible).
>
> This was intended to help people make large posters using printers that
> can only do a single page.
>
> However ...
>
> I do not see why this is necessary. Most tree-drawing programs
should be
> able to write a file that has the large tree plotted on it. If you
don't
> want to print the resulting tree on paper, it would then be possible to
> view the tree in an application such as Adobe Acrobat Reader and
zoom in on
> it and see the tiny branches and their labels. Making multiple
plots for
> one tree would probably confuse the matter.
>
> Or is there something I am missing here?
>
> J.F.
> ----
> Joe Felsenstein j...@gs.washington.edu
> Department of Genome Sciences and Department of Biology,
> University of Washington, Box 355065, Seattle, WA 98195-5065 USA
>
[[alternative HTML version deleted]]
------------------------------
Message: 3
Date: Thu, 5 Mar 2015 04:57:41 -0800
From: Joe Felsenstein <j...@gs.washington.edu>
To: Jonas Eberle <eberle.jo...@gmail.com>
Cc: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] multipage pdf of a huge tree
Message-ID:
<CABXfcPG0H1vZ1P=xhwj2mcmukxbruxtboan_nmvtshlmc5d...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
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. This took me
to the
> limits of this approach, since pdf size is limited to 200 inch by
Adobe and
> there also seems to be a lower limit for font size in pdfs (at least
during
> export form R?).
>
> I didn't knew that Drawtree is able to split the tree over multiple
pages.
> I guess this is an option in the command line version? I will check that
> out. In the mean time I found a way to do the job in R (see my post
before)
> that seems to produce reasonable results.
>
>
PHYLIP programs do not enter settings on the command-line. They have a
menu. The Drawgram and Drawtree programs have a choice that gives a
submenu in which multiple pages can be selected. This submenu is not
available in the GUI (Java front end) version of those programs, but is
available in the character-mode menu that appears if the program is run
from the command line. It is the selection made by typing the character
"#".
J.F.
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
[[alternative HTML version deleted]]
------------------------------
Message: 4
Date: Thu, 05 Mar 2015 08:09:11 -0600
From: Bret Larget <lar...@stat.wisc.edu>
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] multipage pdf of a huge tree
Message-ID: <54f86387.4010...@stat.wisc.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
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 whatever you use, the printing
program will print on multiple pages. Open the tree first before
printing to preview to see if you have adequate space between taxa and
adjust the height as needed. The page breaks may not be great and each
page will have top and bottom margins, but will a scissors and tape, you
can get an okay large single picture.
I imagine, however, that a better way to visualize such a large tree
would be to employ some hierarchy. The first page could show the root
and enough of the tree to show a reasonable number of clades that can
seen easily on a single page. Then each clade could be represented by
its own rooted tree; if any single one is too big for a single page,
then recurse.
-Bret Larget
------------------------------
Message: 5
Date: Thu, 5 Mar 2015 12:57:22 -0300
From: "Alexandre F. Souza" <alexsouza.cb.ufrn...@gmail.com>
To: caetano...@gmail.com
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] Stuck with Phylomatic tree!
Message-ID:
<cafxqfgmz0i8k5j2t_jjdsz5fr0gbyxsvjz7xu_2j3nmowjg...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi Daniel,
Thank you for your reply.
I posted the tree with the note within [] but was not including it when
trying to open it in Phylocom and in R with the newick function. Neither
worked, and I only managed to open it with the rncl package mentioned by
Fran?ois.
Best,
Alexandre
<<attachment: eike_mayland_quellhorst.vcf>>
_______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
