Re: [R-sig-phylo] Query about Phylogenetics in R

[Bhuller, Ravneet]

Dear Liam, Brian and Vojtech,

Many thanks for all your guidance. All this was very helpful.

Many thanks,

Rav




On 31 Aug 2016, at 14:16, Liam J. Revell 
> wrote:

lwd=1,type="fan",fsize=0.7


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Re: [R-sig-phylo] Query about Phylogenetics in R

[Liam J. Revell]

Just to throw out another quick suggestion - for a tree with "only" 220 
tips you could try a "fan" style plot which plots the tip labels 
radially leaving you with a bit more chance of being able to read them.


This is implemented in the plot method for the object class, but also in 
phytools::plotTree. For instance:


plotTree(tree,lwd=1,type="fan",fsize=0.7)

Of course, as Brian suggested you can wrap that it in pdf(...) // 
dev.off() to use a PDF as your plotting device:


pdf(file="mytree.pdf",width=10,height=10)
plot(tree,lwd=1,type="fan",fsize=0.8)
dev.off()

All the best, Liam

Liam J. Revell, Associate 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 8/31/2016 8:03 AM, Brian O'Meara wrote:

A similar solution is to create a pdf:

pdf(file="AwesomeTree.pdf", width=10, height=10)
plot(phy)
dev.off()

As you increase the width and height, the labels become proportionally
smaller. You can probably mess around with cex options, too, but this is
the approach I normally use.

Best,
Brian

___
Brian O'Meara, http://www.brianomeara.info, especially Calendar
, CV
, and Feedback


Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis  (NIMBioS)
Communication Director, Society of Systematic Biologists

On Wed, Aug 31, 2016 at 5:25 AM, Vojtěch Zeisek  wrote:


Hello,
if onlythe readibility of the labels is the issue, what about using svg()
function? It produces a SVG file which You can open in almost any vector
editor (like Inkscape) andmove the labels around. Chech ?svg for possible
settings and play with them little bit. They vary among operating systems.
So You can do something like
svg(...) # Any parameters inside, at least output file name
# All the tree ploting commands...
dev.off() # To save the SVG file to the disc
Check also parameters of function tip.labels() - You can specify font size
or replace the text with some symbol.
(Sorry for being so brief, I don't have exact examples handy)
Yours,
V.


31. srpna 2016 11:11:33 CEST, "Bhuller, Ravneet" <
ravneet.bhulle...@imperial.ac.uk> napsal:

Dear All,

I am trying to construct a phylogenetic tree (neighbour joining) using
either APE or PHANGORN in R. But, since I have got 220 strains of
bacteria in my data, the resulted tree is not very clear. The branch
labels are so much overlapping that they cannot be read at all. Is
there any way, I can get a neat tree with clearly read labels? Any
guidance will be very much appreciated.

Regards,

Rav

--
Vojtěch Zeisek
http://trapa.cz/cs

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Re: [R-sig-phylo] Query about Phylogenetics in R

[Brian O'Meara]

A similar solution is to create a pdf:

pdf(file="AwesomeTree.pdf", width=10, height=10)
plot(phy)
dev.off()

As you increase the width and height, the labels become proportionally
smaller. You can probably mess around with cex options, too, but this is
the approach I normally use.

Best,
Brian

___
Brian O'Meara, http://www.brianomeara.info, especially Calendar
, CV
, and Feedback


Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis  (NIMBioS)
Communication Director, Society of Systematic Biologists

On Wed, Aug 31, 2016 at 5:25 AM, Vojtěch Zeisek  wrote:

> Hello,
> if onlythe readibility of the labels is the issue, what about using svg()
> function? It produces a SVG file which You can open in almost any vector
> editor (like Inkscape) andmove the labels around. Chech ?svg for possible
> settings and play with them little bit. They vary among operating systems.
> So You can do something like
> svg(...) # Any parameters inside, at least output file name
> # All the tree ploting commands...
> dev.off() # To save the SVG file to the disc
> Check also parameters of function tip.labels() - You can specify font size
> or replace the text with some symbol.
> (Sorry for being so brief, I don't have exact examples handy)
> Yours,
> V.
>
>
> 31. srpna 2016 11:11:33 CEST, "Bhuller, Ravneet" <
> ravneet.bhulle...@imperial.ac.uk> napsal:
> >Dear All,
> >
> >I am trying to construct a phylogenetic tree (neighbour joining) using
> >either APE or PHANGORN in R. But, since I have got 220 strains of
> >bacteria in my data, the resulted tree is not very clear. The branch
> >labels are so much overlapping that they cannot be read at all. Is
> >there any way, I can get a neat tree with clearly read labels? Any
> >guidance will be very much appreciated.
> >
> >Regards,
> >
> >Rav
> --
> Vojtěch Zeisek
> http://trapa.cz/cs
>
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> sig-ph...@r-project.org/
>

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Re: [R-sig-phylo] Query about Phylogenetics in R

[Vojtěch Zeisek]

Hello,
if onlythe readibility of the labels is the issue, what about using svg() 
function? It produces a SVG file which You can open in almost any vector editor 
(like Inkscape) andmove the labels around. Chech ?svg for possible settings and 
play with them little bit. They vary among operating systems. So You can do 
something like
svg(...) # Any parameters inside, at least output file name
# All the tree ploting commands...
dev.off() # To save the SVG file to the disc
Check also parameters of function tip.labels() - You can specify font size or 
replace the text with some symbol.
(Sorry for being so brief, I don't have exact examples handy)
Yours,
V.


31. srpna 2016 11:11:33 CEST, "Bhuller, Ravneet" 
 napsal:
>Dear All,
>
>I am trying to construct a phylogenetic tree (neighbour joining) using
>either APE or PHANGORN in R. But, since I have got 220 strains of
>bacteria in my data, the resulted tree is not very clear. The branch
>labels are so much overlapping that they cannot be read at all. Is
>there any way, I can get a neat tree with clearly read labels? Any
>guidance will be very much appreciated.
>
>Regards,
>
>Rav
-- 
Vojtěch Zeisek
http://trapa.cz/cs

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