AFAIK almost any modern browser can render SVG natively - this is not the case
for PDF, which will often require a plug-in from adobe.
I don’t think I’ve seen this before, but you could probably generate
web-friendly vector tree figures using SVG - there are options to explore this
in adobe illu
Hi Eike,
I didn't intend to print the tree. I think a pdf is the most convenient
format for publishing since nearly everybody can easily open it on every
operating system and it always looks the same. I've never tried to open a
large tree in an svg in a browser. Maybe that's fine, too.
All the be
--
Message: 1
Date: Thu, 5 Mar 2015 03:41:38 -0800
From: Joe Felsenstein
To: Jonas Eberle
Cc: "r-sig-phylo@r-project.org"
Subject: Re: [R-sig-phylo] multipage pdf of a huge tree
Message-ID:
Content-Type: text/plain; charset="UTF-8"
Jonas Eberle wrote:
>
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?
>> ax
Mind=Blown.
Amazing. Thank you.
Jake
> On Mar 5, 2015, at 2:55 PM, Liam J. Revell 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 example, some th
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 position
Hi Liam,
Would there be a way to modify this so that annotations like node labels and
axes could be applied to both 1/2s of a split tree at the same time? I’ve been
struggling with a similar problem using plot.phylo() and we can get our tree to
look like what we want on one page, but splitting
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 :
> Hi Jonas.
>
> I thought of the same thing. Unfortunately, one thing that I discovered is
> that because R au
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
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 whateve
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
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
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?
>
;> blog: http://blog.phytools.org
>> ---
>> Sent from my Windows Phone
>> --
>> From: Jonas Eberle
>> Sent: 3/4/2015 12:14 PM
>> To: r-sig-phylo@r-project.org
>> Subject: [R-sig-phylo] multipage pdf of a huge tree
>>
/liam.revell
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
> ---
> Sent from my Windows Phone
> --
> From: Jonas Eberle
> Sent: 3/4/2015 12:14 PM
> To: r-sig-phylo@r-project.org
> Subject: [R-sig-phylo] multipage pdf of a huge tre
.jo...@gmail.com>
Sent: �3/�4/�2015 12:14 PM
To: r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] multipage pdf of a huge tree
Dear all,
I'm searching for a way to plot a huge phylogenetic tree to multiple pages
in one searchable pdf file from R.
I tho
Dear all,
I'm searching for a way to plot a huge phylogenetic tree to multiple pages
in one searchable pdf file from R.
I thought of something like:
1. opening a pdf file
2. plotting a 'clipped' part of the tree (e.g. tips 1-100) as the first
figure on page one
3. plotting the next part of the tre
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