Re: [R-sig-phylo] pPCA - global and local components
That seems like it would be OK, at least if you think it is OK for nonphylogenetic PCA. An alternative is to simulate data along your phylogeny, analyze it the same way, do it a couple thousand times, then make an empirical null distribution of, say, the eigenvalues when the data have no correlation on average but increased variance in the values of correlations caused by the phylogenetic hierarchy. This is discussed in our very old PHYLOGR package. However, you will need to make some decisions about the "branch lengths" to use for your individuals within species, represented by a bunch of mini-star phylogenies. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwJ Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Franck Stefani [fopstef...@gmail.com] Sent: Wednesday, August 22, 2012 3:50 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] pPCA - global and local components Hi, Among the graphical outputs of the pPCA, there is the scree plot showing the global and local components. I would like to know what are the criteria to define the number of GPC or LPC to interpret ? Can we use a broken stick model? Cheers, Franck [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] pPCA - global and local components
Hi, Among the graphical outputs of the pPCA, there is the scree plot showing the global and local components. I would like to know what are the criteria to define the number of GPC or LPC to interpret ? Can we use a broken stick model? Cheers, Franck [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] plotting a coloured tree
Many thanks Marcio and Emmanuel!
That solved my problems to plot the tree.
2012/8/22 Emmanuel Paradis
> Agus,
>
> Whether the background appears transparent or not depends on the device
> where you plot the tree. On Linux, the default device (X11) is transparent:
>
> par("bg")
>>
> [1] "transparent"
>
> When plotting in a file, the default depends on the file format: pdf() has
> transparent background, but png() has a white one. For the latter you may
> do:
>
> png("tree.png")
> par(bg = "transparent")
> plot(tree, ... etc...
> dev.off()
>
> The way the background is rendered may depend on the application you use
> to open this file: on my system the transparent background of a PNG image
> is shown as a grey checkerboard, but when I open a PDF file with a
> transparent background, this one appears white. But the difference between
> a transparent and a white background should be clear if you include such a
> file in a document or in slides.
>
> Best,
>
> Emmanuel
>
> Marcio Pie wrote on 20/08/2012 07:09:
>
>> Hi Agustin,
>>
>> The problem seems to be the space between the genus and the species
>> names. Try this:
>>
>>
>> require(ape)
>> require(geiger)
>>
>> tree<-read.tree(text="
>> Calyptommatus_leiolepis:0.**0168, Calyptommatus_nicterus:0.0099)**
>> :0.0242
>> ,Calyptommatus_sinebrachiatus:**0.038):0.0724
>> ,(Scriptosaura_catimbau:0.022,**Nothobachia_ablephara:0.0309):**
>> 0.0648):0.0659
>> ,Procellosaurinus_**erythrocercus:0.0235,
>> Procellosaurinus_**tetradactylus:0.0259):0.0462
>> ,Vanzosaura_rubricauda:0.072):**0.142
>> ,Micrablepharus_maximiliani:0.**863):0.0225
>> ,Psilopthalmus_paeminosus:0.**193):0.0131);")
>>
>> rgb(red=0, green=0, blue=0, alpha=100, max=255)
>> plot(tree,use.edge.length = T, font=4,tip.col="black", bg="transparent",
>> cex=1.5,edge.color = 'cyan',edge.width = 3)
>>
>>
>> Marcio
>>
>> On Sun, Aug 19, 2012 at 8:19 PM, Agus Camacho
>> wrote:
>>
>>> Dear list,
>>>
>>>
>>> Im trying to plot a coloured tree with transparent background, to do
>>> that,
>>> im using the following script:
>>> require(ape)
>>> require(geiger)
>>> tree<- read.tree(text="
>>> Calyptommatus leiolepis:0.0168, Calyptommatus nicterus:0.0099):0.0242
>>> ,Calyptommatus sinebrachiatus:0.038):0.0724
>>> ,(Scriptosaura catimbau:0.022,Nothobachia ablephara:0.0309):0.0648):0.**
>>> 0659
>>> ,Procellosaurinus erythrocercus:0.0235,**Procellosaurinus
>>> tetradactylus:0.0259):0.0462
>>> ,Vanzosaura rubricauda:0.072):0.142
>>> ,Micrablepharus maximiliani:0.863):0.0225
>>> ,Psilopthalmus paeminosus:0.193):0.0131);")
>>> rgb(red=0, green=0, blue=0, alpha=100, max=255)
>>> plot(tree,use.edge.length = T, font=4,tip.col="black", bg="transparent",
>>> cex=1.5,edge.color = 'cyan',edge.width = 3)
>>>
>>> However, when I plot that, it does not appear transparent background and
>>> it
>>> also plots together the species name and the genus.
>>> Anybody knows how to do that?
>>> Thanks in advance!
>>> Agus
>>> --
>>> Agustín Camacho Guerrero.
>>> Doutorando em Zoologia.
>>> Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
>>> Biociências, USP.
>>> Rua do Matão, trav. 14, nº 321, Cidade Universitária,
>>> São Paulo - SP, CEP: 05508-090, Brasil.
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>> __**_
>>> R-sig-phylo mailing list
>>> R-sig-phylo@r-project.org
>>> https://stat.ethz.ch/mailman/**listinfo/r-sig-phylo
>>>
>>>
>>
>>
>>
> --
> Emmanuel Paradis
> IRD, Jakarta, Indonesia
> http://ape.mpl.ird.fr/
>
--
Agustín Camacho Guerrero.
Doutorando em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
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Re: [R-sig-phylo] plotting a coloured tree
Agus,
Whether the background appears transparent or not depends on the device
where you plot the tree. On Linux, the default device (X11) is transparent:
par("bg")
[1] "transparent"
When plotting in a file, the default depends on the file format: pdf()
has transparent background, but png() has a white one. For the latter
you may do:
png("tree.png")
par(bg = "transparent")
plot(tree, ... etc...
dev.off()
The way the background is rendered may depend on the application you use
to open this file: on my system the transparent background of a PNG
image is shown as a grey checkerboard, but when I open a PDF file with a
transparent background, this one appears white. But the difference
between a transparent and a white background should be clear if you
include such a file in a document or in slides.
Best,
Emmanuel
Marcio Pie wrote on 20/08/2012 07:09:
Hi Agustin,
The problem seems to be the space between the genus and the species
names. Try this:
require(ape)
require(geiger)
tree<-read.tree(text="
Calyptommatus_leiolepis:0.0168, Calyptommatus_nicterus:0.0099):0.0242
,Calyptommatus_sinebrachiatus:0.038):0.0724
,(Scriptosaura_catimbau:0.022,Nothobachia_ablephara:0.0309):0.0648):0.0659
,Procellosaurinus_erythrocercus:0.0235,
Procellosaurinus_tetradactylus:0.0259):0.0462
,Vanzosaura_rubricauda:0.072):0.142
,Micrablepharus_maximiliani:0.863):0.0225
,Psilopthalmus_paeminosus:0.193):0.0131);")
rgb(red=0, green=0, blue=0, alpha=100, max=255)
plot(tree,use.edge.length = T, font=4,tip.col="black", bg="transparent",
cex=1.5,edge.color = 'cyan',edge.width = 3)
Marcio
On Sun, Aug 19, 2012 at 8:19 PM, Agus Camacho wrote:
Dear list,
Im trying to plot a coloured tree with transparent background, to do that,
im using the following script:
require(ape)
require(geiger)
tree<- read.tree(text="
Calyptommatus leiolepis:0.0168, Calyptommatus nicterus:0.0099):0.0242
,Calyptommatus sinebrachiatus:0.038):0.0724
,(Scriptosaura catimbau:0.022,Nothobachia ablephara:0.0309):0.0648):0.0659
,Procellosaurinus erythrocercus:0.0235,Procellosaurinus
tetradactylus:0.0259):0.0462
,Vanzosaura rubricauda:0.072):0.142
,Micrablepharus maximiliani:0.863):0.0225
,Psilopthalmus paeminosus:0.193):0.0131);")
rgb(red=0, green=0, blue=0, alpha=100, max=255)
plot(tree,use.edge.length = T, font=4,tip.col="black", bg="transparent",
cex=1.5,edge.color = 'cyan',edge.width = 3)
However, when I plot that, it does not appear transparent background and it
also plots together the species name and the genus.
Anybody knows how to do that?
Thanks in advance!
Agus
--
Agustín Camacho Guerrero.
Doutorando em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
[[alternative HTML version deleted]]
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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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