Re: [R-sig-phylo] multipage pdf of a huge tree
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 illustrator if you have it. Jake > On Mar 8, 2015, at 12:06 PM, Jonas Eberle wrote: > > 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 best, > Jonas > > [[alternative HTML version deleted]] > > ___ > 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/ Jacob Berv Ph.D. Student Lovette Lab Cornell Laboratory of Ornithology ___ 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/
Re: [R-sig-phylo] multipage pdf of a huge tree
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 best, Jonas [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] multipage pdf of a huge tree
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 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: > 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 To: Joe Felsenstein 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" 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 :
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?
>> axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col =
>> c("grey80", "white"), texcol = "black", gridty = 2, gridcol = "red",
>> ages=TRUE)
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 things like node & edge labels
> are split across pages - in which case you can fiddle with the split
> positions & replot the tree until it is the way you want it.
>
> All the best, Liam
>
> Liam J. Revell, Assistant Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
>
> On 3/5/2015 2:24 PM, Jacob Berv wrote:
>> 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 it up while
>> keeping node and branch annotations etc is problematic.
>>
>> For example, I am trying to plot a tree and annotate with the following
>> function calls.
>>
>> #from ape
>> plot.phylo(timetree, cex=0.315, label.offset=0.35, edge.width=1.25,
>> edge.color=color)
>>
>> #from phyloch - adds a geologic time scale
>> axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col =
>> c("grey80", "white"), texcol = "black", gridty = 2, gridcol = "red",
>> ages=TRUE)
>>
>> #then additional annotations with:
>> nodelabels()
>> axis()
>>
>> I want to cut my tree in 1/2 and plot each 1/2 on a separate page, but
>> maintain the axes and annotations. Splitting a tree is great but it’s not
>> super useful unless you can call other functions on the pieces. It would be
>> great to be able to generate axes for each piece of a split tree
>> independently and then annotate each one as if they were a separate plot.
>>
>> Jake
>>
>>
>>
>>> On Mar 5, 2015, at 11:46 AM, Jonas Eberle wrote:
>>>
>>> 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 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 species or edges
near the bottom or top of each page, you may find what I did.
I have posted a solution to this here: http://blog.phytools.org/2015/
03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from
phytools internally, but it could fairly easily be modified to use other
tree plotters such as plot.phylo or plotSimmap.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2015 5:19 AM, Jonas Eberle wrote:
> MultipagePhyloPlot <- function (tree, npages = 5) {
> ntips <- length(tree$tip.label)
> tips.per.page <- ntips / npages
> y1 <- ntips - tips.per.page
> y2 <- ntips
> for (i in 1:npages) {
> plot.phylo(tree, y.lim = c(y1, y2))
> y1 <- y1 - tips.per.page
> y2 <- y2 - tips.per.page
> }
> }
>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> 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/
>>
>> Jacob Berv
>>
>> Ph.D. Student
>> Lovette Lab
>> Cornell Laboratory of Ornithology
>>
___
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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 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 things like node & edge labels
> are split across pages - in which case you can fiddle with the split
> positions & replot the tree until it is the way you want it.
>
> All the best, Liam
>
> Liam J. Revell, Assistant Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
>
> On 3/5/2015 2:24 PM, Jacob Berv wrote:
>> 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 it up while
>> keeping node and branch annotations etc is problematic.
>>
>> For example, I am trying to plot a tree and annotate with the following
>> function calls.
>>
>> #from ape
>> plot.phylo(timetree, cex=0.315, label.offset=0.35, edge.width=1.25,
>> edge.color=color)
>>
>> #from phyloch - adds a geologic time scale
>> axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col =
>> c("grey80", "white"), texcol = "black", gridty = 2, gridcol = "red",
>> ages=TRUE)
>>
>> #then additional annotations with:
>> nodelabels()
>> axis()
>>
>> I want to cut my tree in 1/2 and plot each 1/2 on a separate page, but
>> maintain the axes and annotations. Splitting a tree is great but it’s not
>> super useful unless you can call other functions on the pieces. It would be
>> great to be able to generate axes for each piece of a split tree
>> independently and then annotate each one as if they were a separate plot.
>>
>> Jake
>>
>>
>>
>>> On Mar 5, 2015, at 11:46 AM, Jonas Eberle wrote:
>>>
>>> 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 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 species or edges
near the bottom or top of each page, you may find what I did.
I have posted a solution to this here: http://blog.phytools.org/2015/
03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from
phytools internally, but it could fairly easily be modified to use other
tree plotters such as plot.phylo or plotSimmap.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2015 5:19 AM, Jonas Eberle wrote:
> MultipagePhyloPlot <- function (tree, npages = 5) {
> ntips <- length(tree$tip.label)
> tips.per.page <- ntips / npages
> y1 <- ntips - tips.per.page
> y2 <- ntips
> for (i in 1:npages) {
> plot.phylo(tree, y.lim = c(y1, y2))
> y1 <- y1 - tips.per.page
> y2 <- y2 - tips.per.page
> }
> }
>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> 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/
>>
>> Jacob Berv
>>
>> Ph.D. Student
>> Lovette Lab
>> Cornell Laboratory of Ornithology
>>
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
___
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Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
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 positions & replot the tree until it is the way you want it.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2015 2:24 PM, Jacob Berv wrote:
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 it up while keeping node and
branch annotations etc is problematic.
For example, I am trying to plot a tree and annotate with the following
function calls.
#from ape
plot.phylo(timetree, cex=0.315, label.offset=0.35, edge.width=1.25,
edge.color=color)
#from phyloch - adds a geologic time scale
axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col = c("grey80", "white"), texcol
= "black", gridty = 2, gridcol = "red", ages=TRUE)
#then additional annotations with:
nodelabels()
axis()
I want to cut my tree in 1/2 and plot each 1/2 on a separate page, but maintain
the axes and annotations. Splitting a tree is great but it’s not super useful
unless you can call other functions on the pieces. It would be great to be able
to generate axes for each piece of a split tree independently and then annotate
each one as if they were a separate plot.
Jake
On Mar 5, 2015, at 11:46 AM, Jonas Eberle wrote:
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 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 species or edges
near the bottom or top of each page, you may find what I did.
I have posted a solution to this here: http://blog.phytools.org/2015/
03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from
phytools internally, but it could fairly easily be modified to use other
tree plotters such as plot.phylo or plotSimmap.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2015 5:19 AM, Jonas Eberle wrote:
MultipagePhyloPlot <- function (tree, npages = 5) {
ntips <- length(tree$tip.label)
tips.per.page <- ntips / npages
y1 <- ntips - tips.per.page
y2 <- ntips
for (i in 1:npages) {
plot.phylo(tree, y.lim = c(y1, y2))
y1 <- y1 - tips.per.page
y2 <- y2 - tips.per.page
}
}
[[alternative HTML version deleted]]
___
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https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
___
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Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] multipage pdf of a huge tree
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 it up while keeping node and
branch annotations etc is problematic.
For example, I am trying to plot a tree and annotate with the following
function calls.
#from ape
plot.phylo(timetree, cex=0.315, label.offset=0.35, edge.width=1.25,
edge.color=color)
#from phyloch - adds a geologic time scale
axisGeo(GTS = strat2012, unit = c("epoch", "period"), cex = 0.7, col =
c("grey80", "white"), texcol = "black", gridty = 2, gridcol = "red", ages=TRUE)
#then additional annotations with:
nodelabels()
axis()
I want to cut my tree in 1/2 and plot each 1/2 on a separate page, but maintain
the axes and annotations. Splitting a tree is great but it’s not super useful
unless you can call other functions on the pieces. It would be great to be able
to generate axes for each piece of a split tree independently and then annotate
each one as if they were a separate plot.
Jake
> On Mar 5, 2015, at 11:46 AM, Jonas Eberle wrote:
>
> 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 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 species or edges
>> near the bottom or top of each page, you may find what I did.
>>
>> I have posted a solution to this here: http://blog.phytools.org/2015/
>> 03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from
>> phytools internally, but it could fairly easily be modified to use other
>> tree plotters such as plot.phylo or plotSimmap.
>>
>> All the best, Liam
>>
>> Liam J. Revell, Assistant Professor of Biology
>> University of Massachusetts Boston
>> web: http://faculty.umb.edu/liam.revell/
>> email: liam.rev...@umb.edu
>> blog: http://blog.phytools.org
>>
>> On 3/5/2015 5:19 AM, Jonas Eberle wrote:
>>
>>> MultipagePhyloPlot <- function (tree, npages = 5) {
>>> ntips <- length(tree$tip.label)
>>> tips.per.page <- ntips / npages
>>> y1 <- ntips - tips.per.page
>>> y2 <- ntips
>>> for (i in 1:npages) {
>>> plot.phylo(tree, y.lim = c(y1, y2))
>>> y1 <- y1 - tips.per.page
>>> y2 <- y2 - tips.per.page
>>> }
>>> }
>>>
>>
>
> [[alternative HTML version deleted]]
>
> ___
> 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/
Jacob Berv
Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology
___
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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 :
> 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 species or edges
> near the bottom or top of each page, you may find what I did.
>
> I have posted a solution to this here: http://blog.phytools.org/2015/
> 03/splitting-tree-over-mutiple-plotting.html. It uses plotTree from
> phytools internally, but it could fairly easily be modified to use other
> tree plotters such as plot.phylo or plotSimmap.
>
> All the best, Liam
>
> Liam J. Revell, Assistant Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
>
> On 3/5/2015 5:19 AM, Jonas Eberle wrote:
>
>> MultipagePhyloPlot <- function (tree, npages = 5) {
>>ntips <- length(tree$tip.label)
>>tips.per.page <- ntips / npages
>>y1 <- ntips - tips.per.page
>>y2 <- ntips
>>for (i in 1:npages) {
>> plot.phylo(tree, y.lim = c(y1, y2))
>> y1 <- y1 - tips.per.page
>> y2 <- y2 - tips.per.page
>>}
>> }
>>
>
[[alternative HTML version deleted]]
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Re: [R-sig-phylo] multipage pdf of a huge tree
Hi Jonas.
I thought of the same thing. Unfortunately, one thing that I discovered
is that because R automatically adds 4% or so to the plotting range, you
will find that species & edges near the bottom of one page will also
appear at the top of the next page. If you test your code & look for
species or edges near the bottom or top of each page, you may find what
I did.
I have posted a solution to this here:
http://blog.phytools.org/2015/03/splitting-tree-over-mutiple-plotting.html.
It uses plotTree from phytools internally, but it could fairly easily be
modified to use other tree plotters such as plot.phylo or plotSimmap.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/5/2015 5:19 AM, Jonas Eberle wrote:
MultipagePhyloPlot <- function (tree, npages = 5) {
ntips <- length(tree$tip.label)
tips.per.page <- ntips / npages
y1 <- ntips - tips.per.page
y2 <- ntips
for (i in 1:npages) {
plot.phylo(tree, y.lim = c(y1, y2))
y1 <- y1 - tips.per.page
y2 <- y2 - tips.per.page
}
}
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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 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 ___ 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/
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. 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]] ___ 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/
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 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 : > > 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]] ___ 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/
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? > 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]] ___ 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/
Re: [R-sig-phylo] multipage pdf of a huge tree
Hi all,
I found the ylim option in plot.phylo(). With a simple loop we can
distribute the tree on multiple pages:
MultipagePhyloPlot <- function (tree, npages = 5) {
ntips <- length(tree$tip.label)
tips.per.page <- ntips / npages
y1 <- ntips - tips.per.page
y2 <- ntips
for (i in 1:npages) {
plot.phylo(tree, y.lim = c(y1, y2))
y1 <- y1 - tips.per.page
y2 <- y2 - tips.per.page
}
}
It's saved to a pdf with something like:
pdf("multipageplot.pdf", paper="a4", onefile=T)
MultipagePhyloPlot(tree, npages=5)
dev.off()
Thanks again for helping! R is great!
All the best,
Jonas
--
Jonas Eberle
PhD student
2015-03-05 10:06 GMT+01:00 Jonas Eberle :
> 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 the best,
> Jonas
>
> --
> Jonas Eberle
> PhD student
>
> 2015-03-04 18:31 GMT+01:00 Liam Revell :
>
>> Hi Jonas.
>>
>> One option is to use the function splitPlotTree in phytools. By default
>> it plots the split tree in two columns, but there is an option to split it
>> into two windows. Then each plotted tree could be saved as a PDF.
>>
>> I will also investigate this to see if there is a better possibility.
>>
>> All the best,
>>
>> Liam J. Revell, Assistant Professor of Biology
>> University of Massachusetts Boston
>> web: http://faculty.umb.edu/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 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 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 tree (tips 101-200) as the second figure
>> on page two and so on...
>> 4. closing the pdf file.
>>
>> However, clip() seems not to work with plot.phylo() from ape. I tried:
>>
>> library(phytools)
>> tree <- tree<-pbtree(n=100,scale=1)
>> plot.new()
>> clip(x1=0, x2=1, y1=1, y2=50)
>> par(new = TRUE)
>> plot.phylo(tree)
>> axis(side=1); axis(side=2)
>>
>> Does anybody know if this is possible and an effective way of doing this?
>> Depending on the method of clipping (if there is more than one available),
>> is the whole tree plotted internally in each step or even worse hiddenly
>> embedded in the pdf?
>>
>> Thank you very much for your help!
>>
>> Jonas
>>
>> --
>> Jonas Eberle
>> PhD student
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> 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/
>>
>
>
[[alternative HTML version deleted]]
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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 the best, Jonas -- Jonas Eberle PhD student 2015-03-04 18:31 GMT+01:00 Liam Revell : > Hi Jonas. > > One option is to use the function splitPlotTree in phytools. By default it > plots the split tree in two columns, but there is an option to split it > into two windows. Then each plotted tree could be saved as a PDF. > > I will also investigate this to see if there is a better possibility. > > All the best, > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/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 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 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 tree (tips 101-200) as the second figure > on page two and so on... > 4. closing the pdf file. > > However, clip() seems not to work with plot.phylo() from ape. I tried: > > library(phytools) > tree <- tree<-pbtree(n=100,scale=1) > plot.new() > clip(x1=0, x2=1, y1=1, y2=50) > par(new = TRUE) > plot.phylo(tree) > axis(side=1); axis(side=2) > > Does anybody know if this is possible and an effective way of doing this? > Depending on the method of clipping (if there is more than one available), > is the whole tree plotted internally in each step or even worse hiddenly > embedded in the pdf? > > Thank you very much for your help! > > Jonas > > -- > Jonas Eberle > PhD student > > [[alternative HTML version deleted]] > > ___ > 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/ > [[alternative HTML version deleted]] ___ 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/
Re: [R-sig-phylo] multipage pdf of a huge tree
Hi Jonas. One option is to use the function splitPlotTree in phytools. By default it plots the split tree in two columns, but there is an option to split it into two windows. Then each plotted tree could be saved as a PDF. I will also investigate this to see if there is a better possibility. All the best, Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell email: liam.rev...@umb.edu blog: http://blog.phytools.org --- Sent from my Windows Phone From: Jonas Eberle<mailto:eberle.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 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 tree (tips 101-200) as the second figure on page two and so on... 4. closing the pdf file. However, clip() seems not to work with plot.phylo() from ape. I tried: library(phytools) tree <- tree<-pbtree(n=100,scale=1) plot.new() clip(x1=0, x2=1, y1=1, y2=50) par(new = TRUE) plot.phylo(tree) axis(side=1); axis(side=2) Does anybody know if this is possible and an effective way of doing this? Depending on the method of clipping (if there is more than one available), is the whole tree plotted internally in each step or even worse hiddenly embedded in the pdf? Thank you very much for your help! Jonas -- Jonas Eberle PhD student [[alternative HTML version deleted]] ___ 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/ [[alternative HTML version deleted]] ___ 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/
[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 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 tree (tips 101-200) as the second figure on page two and so on... 4. closing the pdf file. However, clip() seems not to work with plot.phylo() from ape. I tried: library(phytools) tree <- tree<-pbtree(n=100,scale=1) plot.new() clip(x1=0, x2=1, y1=1, y2=50) par(new = TRUE) plot.phylo(tree) axis(side=1); axis(side=2) Does anybody know if this is possible and an effective way of doing this? Depending on the method of clipping (if there is more than one available), is the whole tree plotted internally in each step or even worse hiddenly embedded in the pdf? Thank you very much for your help! Jonas -- Jonas Eberle PhD student [[alternative HTML version deleted]] ___ 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/
