[MORPHMET] A question about PCA in geomorph

2015-04-11 Thread Mauro Cavalcanti 
Dear ALL,

I have a number of questions about the geomorph R package, that I will post
here in separate messages.

First one concerns Principal Components Analysis, using the
plotTangentSpace routine. It requires a 3D matrix as argument, however my
data (on fishes) are 2D and I could not figure out how to convert my data
to the required format; the explanation of the arrayspecs routine in the
"Quick Guide to Geomorph" was not clear for me (and it lacks a workin
exemple).

My data are read from a NTSYSpc file containing 2D coordinates for 10
landmarks for a number of fish specimens, using the readland.nts routine. I
have been able to perform a PCA on these data using the shapepca routine in
Ian Dryden's shapes R package, but would like to perfom the entire analysis
using geomorph.

Thanks in advance for any hints!

Best regards,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Mauro Cavalcanti 
Dear Emma & ALL,

Indeed, when reading my data with readland.nts I get the data in the format
required by the geomorph analytical routines. The problem is that I was
calling by mistake a routine from Ian Dryden's shapes package (procGPA) to
generate the Procrustes-aligned coordinates, instead of the gpagen routine.
Fixed this and now everything works fine.

I take this opportunity to ask another question, this time relating to the
plots generated by geomorph. Is there a way to customize them, including
for example axis labels in the PCA plots? In fact, the "Quick Guide" shows
these plots with labels, but I could not figure out how to include them in
my plots. Calling the R par function (as one should have done when using
the usual "plot" command) did not work.

Again, thanks for your help.

Best regards,.

2015-04-12 1:39 GMT-03:00 Emma Sherratt :

> Mauro,
>
> If you read in your NTS data file using readland.nts, it will
> automatically be in the 3D array format required by plotTangentSpace (after
> you use gpagen to do a Procrustes Superimposition).
>
> If you have your data as a 2D matrix, you simply use arrayspecs to make it
> a 3D array.
>
> Emma
>
> On Sunday, April 12, 2015, Mauro Cavalcanti  wrote:
>
>> Dear ALL,
>>
>> I have a number of questions about the geomorph R package, that I will
>> post here in separate messages.
>>
>> First one concerns Principal Components Analysis, using the
>> plotTangentSpace routine. It requires a 3D matrix as argument, however my
>> data (on fishes) are 2D and I could not figure out how to convert my data
>> to the required format; the explanation of the arrayspecs routine in the
>> "Quick Guide to Geomorph" was not clear for me (and it lacks a workin
>> exemple).
>>
>> My data are read from a NTSYSpc file containing 2D coordinates for 10
>> landmarks for a number of fish specimens, using the readland.nts routine. I
>> have been able to perform a PCA on these data using the shapepca routine in
>> Ian Dryden's shapes R package, but would like to perfom the entire analysis
>> using geomorph.
>>
>> Thanks in advance for any hints!
>>
>> Best regards,
>>
>> --
>> Dr. Mauro J. Cavalcanti
>> E-mail: mauro...@gmail.com
>> Web: maurobio 
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>>
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org.
>>
>
>
> --
>
> ~~~
>
> Emma Sherratt, PhD.
>
> Lecturer in Zoology,
> Zoology Division, School of Environmental and Rural Science,
> Room L120 Bldg C02,
> University of New England,
> Armidale, NSW, Australia, 2351
> Tel: +61 2 6773 5041
> email: emma.sherr...@une.edu.au
> Twitter: @DrEmSherratt
>
> Caecilians are legless amphibians...
>
> *  __
> (\   .-.   .-.   /_")
>  \\_//^\\_//^\\_//
>   `"`   `"`   `"`*
>
> learn more about them here: www.emmasherratt.com/caecilians
>
>
>
>
>


-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Collyer, Michael 
Mauro,

The extractable parts from prcomp() are also extractable from plotTangentSpace. 
 One can make custom plots, relabel axes, change symbols, etc.  Example:

myplot = plotTangentSpace(mydata)
attributes(myplot) # shows extractable parts

PC.scores = myplot$x

par(…)
plot(PC.scores, …)

Keep in mind with plotTangentSpace, the product is actually multiple plots, as 
the transformation grids are also plots.  Therefore, it is not easy to pass on 
par() input to the result.  But because users can extract the scores, all base 
R plotting functions are available.

Cheers!
-Mike

Michael Collyer

Assistant Professor
Department of Biology
Western Kentucky University
1906 College Heights Blvd. #11080
Bowling Green, KY 42101-1080
Phone: 270-745-8765; Fax: 270-745-6856
Email: michael.coll...@wku.edu

On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti 
mailto:mauro...@gmail.com>> wrote:

Dear Emma & ALL,

Indeed, when reading my data with readland.nts I get the data in the format 
required by the geomorph analytical routines. The problem is that I was calling 
by mistake a routine from Ian Dryden's shapes package (procGPA) to generate the 
Procrustes-aligned coordinates, instead of the gpagen routine. Fixed this and 
now everything works fine.

I take this opportunity to ask another question, this time relating to the 
plots generated by geomorph. Is there a way to customize them, including for 
example axis labels in the PCA plots? In fact, the "Quick Guide" shows these 
plots with labels, but I could not figure out how to include them in my plots. 
Calling the R par function (as one should have done when using the usual "plot" 
command) did not work.

Again, thanks for your help.

Best regards,.

2015-04-12 1:39 GMT-03:00 Emma Sherratt 
mailto:emma.sherr...@gmail.com>>:
Mauro,

If you read in your NTS data file using readland.nts, it will automatically be 
in the 3D array format required by plotTangentSpace (after you use gpagen to do 
a Procrustes Superimposition).

If you have your data as a 2D matrix, you simply use arrayspecs to make it a 3D 
array.

Emma

On Sunday, April 12, 2015, Mauro Cavalcanti 
mailto:mauro...@gmail.com>> wrote:
Dear ALL,

I have a number of questions about the geomorph R package, that I will post 
here in separate messages.

First one concerns Principal Components Analysis, using the plotTangentSpace 
routine. It requires a 3D matrix as argument, however my data (on fishes) are 
2D and I could not figure out how to convert my data to the required format; 
the explanation of the arrayspecs routine in the "Quick Guide to Geomorph" was 
not clear for me (and it lacks a workin exemple).

My data are read from a NTSYSpc file containing 2D coordinates for 10 landmarks 
for a number of fish specimens, using the readland.nts routine. I have been 
able to perform a PCA on these data using the shapepca routine in Ian Dryden's 
shapes R package, but would like to perfom the entire analysis using geomorph.

Thanks in advance for any hints!

Best regards,

--
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: maurobio

--
MORPHMET may be accessed via its webpage at 
http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to 
morphmet+unsubscr...@morphometrics.org.


--

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt


Caecilians are legless amphibians...

  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`

learn more about them here: 
www.emmasherratt.com/caecilians






--
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

--
MORPHMET may be accessed via its webpage at 
http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to 
morphmet+unsubscr...@morphometrics.org.

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Collyer, Michael 
Mauro, plus others,

As a follow up, we are also working on a new function in geomorph to allow 
users to modify transformation (deformation) grids.  Much like the R par 
function, this function will allow users to vary the colors, width, and style 
of grid lines and link links, the density of grid points, and the color and 
size of landmarks.  This function will be available in the near future.

Michael Collyer

Assistant Professor
Department of Biology
Western Kentucky University
1906 College Heights Blvd. #11080
Bowling Green, KY 42101-1080
Phone: 270-745-8765; Fax: 270-745-6856
Email: michael.coll...@wku.edu

On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti 
mailto:mauro...@gmail.com>> wrote:

Dear Emma & ALL,

Indeed, when reading my data with readland.nts I get the data in the format 
required by the geomorph analytical routines. The problem is that I was calling 
by mistake a routine from Ian Dryden's shapes package (procGPA) to generate the 
Procrustes-aligned coordinates, instead of the gpagen routine. Fixed this and 
now everything works fine.

I take this opportunity to ask another question, this time relating to the 
plots generated by geomorph. Is there a way to customize them, including for 
example axis labels in the PCA plots? In fact, the "Quick Guide" shows these 
plots with labels, but I could not figure out how to include them in my plots. 
Calling the R par function (as one should have done when using the usual "plot" 
command) did not work.

Again, thanks for your help.

Best regards,.

2015-04-12 1:39 GMT-03:00 Emma Sherratt 
mailto:emma.sherr...@gmail.com>>:
Mauro,

If you read in your NTS data file using readland.nts, it will automatically be 
in the 3D array format required by plotTangentSpace (after you use gpagen to do 
a Procrustes Superimposition).

If you have your data as a 2D matrix, you simply use arrayspecs to make it a 3D 
array.

Emma

On Sunday, April 12, 2015, Mauro Cavalcanti 
mailto:mauro...@gmail.com>> wrote:
Dear ALL,

I have a number of questions about the geomorph R package, that I will post 
here in separate messages.

First one concerns Principal Components Analysis, using the plotTangentSpace 
routine. It requires a 3D matrix as argument, however my data (on fishes) are 
2D and I could not figure out how to convert my data to the required format; 
the explanation of the arrayspecs routine in the "Quick Guide to Geomorph" was 
not clear for me (and it lacks a workin exemple).

My data are read from a NTSYSpc file containing 2D coordinates for 10 landmarks 
for a number of fish specimens, using the readland.nts routine. I have been 
able to perform a PCA on these data using the shapepca routine in Ian Dryden's 
shapes R package, but would like to perfom the entire analysis using geomorph.

Thanks in advance for any hints!

Best regards,

--
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: maurobio

--
MORPHMET may be accessed via its webpage at 
http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


--

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt


Caecilians are legless amphibians...

  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`

learn more about them here: 
www.emmasherratt.com/caecilians






--
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

--
MORPHMET may be accessed via its webpage at 
http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to 
morphmet+unsubscr...@morphometrics.org.

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Tim Astrop 
Cheers Michael, I look forward to playing around with that!

Tim

*Tim Astrop PhD *
Ammonoid Palaeobiology Lab 
Department of Biology & Biochemistry
University of Bath

On 12 April 2015 at 15:52, Collyer, Michael  wrote:

>  Mauro, plus others,
>
>  As a follow up, we are also working on a new function in geomorph to
> allow users to modify transformation (deformation) grids.  Much like the R
> par function, this function will allow users to vary the colors, width, and
> style of grid lines and link links, the density of grid points, and the
> color and size of landmarks.  This function will be available in the near
> future.
>
>   Michael Collyer
>
> Assistant Professor
> Department of Biology
> Western Kentucky University
> 1906 College Heights Blvd. #11080
> Bowling Green, KY 42101-1080
> Phone: 270-745-8765; Fax: 270-745-6856
> Email: michael.coll...@wku.edu
>
>  On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti  wrote:
>
>   Dear Emma & ALL,
>
>  Indeed, when reading my data with readland.nts I get the data in the
> format required by the geomorph analytical routines. The problem is that I
> was calling by mistake a routine from Ian Dryden's shapes package (procGPA)
> to generate the Procrustes-aligned coordinates, instead of the gpagen
> routine. Fixed this and now everything works fine.
>
>  I take this opportunity to ask another question, this time relating to
> the plots generated by geomorph. Is there a way to customize them,
> including for example axis labels in the PCA plots? In fact, the "Quick
> Guide" shows these plots with labels, but I could not figure out how to
> include them in my plots. Calling the R par function (as one should have
> done when using the usual "plot" command) did not work.
>
>  Again, thanks for your help.
>
>  Best regards,.
>
> 2015-04-12 1:39 GMT-03:00 Emma Sherratt :
>
>> Mauro,
>>
>>  If you read in your NTS data file using readland.nts, it will
>> automatically be in the 3D array format required by plotTangentSpace (after
>> you use gpagen to do a Procrustes Superimposition).
>>
>>  If you have your data as a 2D matrix, you simply use arrayspecs to make
>> it a 3D array.
>>
>>  Emma
>>
>> On Sunday, April 12, 2015, Mauro Cavalcanti  wrote:
>>
>>>Dear ALL,
>>>
>>>  I have a number of questions about the geomorph R package, that I will
>>> post here in separate messages.
>>>
>>>  First one concerns Principal Components Analysis, using the
>>> plotTangentSpace routine. It requires a 3D matrix as argument, however my
>>> data (on fishes) are 2D and I could not figure out how to convert my data
>>> to the required format; the explanation of the arrayspecs routine in the
>>> "Quick Guide to Geomorph" was not clear for me (and it lacks a workin
>>> exemple).
>>>
>>>  My data are read from a NTSYSpc file containing 2D coordinates for 10
>>> landmarks for a number of fish specimens, using the readland.nts routine. I
>>> have been able to perform a PCA on these data using the shapepca routine in
>>> Ian Dryden's shapes R package, but would like to perfom the entire analysis
>>> using geomorph.
>>>
>>>  Thanks in advance for any hints!
>>>
>>>  Best regards,
>>>
>>> --
>>> Dr. Mauro J. Cavalcanti
>>> E-mail: mauro...@gmail.com
>>> Web: maurobio 
>>>
>>>  --
>>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>>>
>>>  To unsubscribe from this group and stop receiving emails from it, send
>>> an email to morphmet+unsubscr...@morphometrics.org.
>>>
>>
>>
>> --
>>
>> ~~~
>>
>> Emma Sherratt, PhD.
>>
>> Lecturer in Zoology,
>> Zoology Division, School of Environmental and Rural Science,
>> Room L120 Bldg C02,
>> University of New England,
>> Armidale, NSW, Australia, 2351
>> Tel: +61 2 6773 5041
>> email: emma.sherr...@une.edu.au
>> Twitter: @DrEmSherratt
>>
>>  Caecilians are legless amphibians...
>>
>> *  __
>> (\   .-.   .-.   /_")
>>  \\_//^\\_//^\\_//
>>   `"`   `"`   `"`*
>>
>> learn more about them here: www.emmasherratt.com/caecilians
>>
>>
>>
>>
>>
>
>
> --
> Dr. Mauro J. Cavalcanti
> E-mail: mauro...@gmail.com
> Web: http://sites.google.com/site/maurobio
>
>  --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
>  To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>
>
>   --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Mauro Cavalcanti 
Michael,

Thanks for your helpful message. Indeed, after posting my question about
plot customization, I was able to generate a PCA plot from plotTangentSpace
with axes labels, using the "par" function immediately before calling the
plotTangentSpace routine, as follows: par(xlab="PC 1", ylab="PC 2").
Obviously, the solution you suggested is even more generic and flexible and
it also works fine.

When means are available to customize the display of deformation grids,
then geomorph will be near perfection!

Thanks again for your help.

With best regards,

2015-04-12 11:19 GMT-03:00 Collyer, Michael :

>  Mauro,
>
>  The extractable parts from prcomp() are also extractable from
> plotTangentSpace.  One can make custom plots, relabel axes, change symbols,
> etc.  Example:
>
>  myplot = plotTangentSpace(mydata)
> attributes(myplot) # shows extractable parts
>
>  PC.scores = myplot$x
>
>  par(…)
> plot(PC.scores, …)
>
>  Keep in mind with plotTangentSpace, the product is actually multiple
> plots, as the transformation grids are also plots.  Therefore, it is not
> easy to pass on par() input to the result.  But because users can extract
> the scores, all base R plotting functions are available.
>
>  Cheers!
> -Mike
>
>  Michael Collyer
>
> Assistant Professor
> Department of Biology
> Western Kentucky University
> 1906 College Heights Blvd. #11080
> Bowling Green, KY 42101-1080
> Phone: 270-745-8765; Fax: 270-745-6856
> Email: michael.coll...@wku.edu
>
>  On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti  wrote:
>
>   Dear Emma & ALL,
>
>  Indeed, when reading my data with readland.nts I get the data in the
> format required by the geomorph analytical routines. The problem is that I
> was calling by mistake a routine from Ian Dryden's shapes package (procGPA)
> to generate the Procrustes-aligned coordinates, instead of the gpagen
> routine. Fixed this and now everything works fine.
>
>  I take this opportunity to ask another question, this time relating to
> the plots generated by geomorph. Is there a way to customize them,
> including for example axis labels in the PCA plots? In fact, the "Quick
> Guide" shows these plots with labels, but I could not figure out how to
> include them in my plots. Calling the R par function (as one should have
> done when using the usual "plot" command) did not work.
>
>  Again, thanks for your help.
>
>  Best regards,.
>
> 2015-04-12 1:39 GMT-03:00 Emma Sherratt :
>
>> Mauro,
>>
>>  If you read in your NTS data file using readland.nts, it will
>> automatically be in the 3D array format required by plotTangentSpace (after
>> you use gpagen to do a Procrustes Superimposition).
>>
>>  If you have your data as a 2D matrix, you simply use arrayspecs to make
>> it a 3D array.
>>
>>  Emma
>>
>> On Sunday, April 12, 2015, Mauro Cavalcanti  wrote:
>>
>>>Dear ALL,
>>>
>>>  I have a number of questions about the geomorph R package, that I will
>>> post here in separate messages.
>>>
>>>  First one concerns Principal Components Analysis, using the
>>> plotTangentSpace routine. It requires a 3D matrix as argument, however my
>>> data (on fishes) are 2D and I could not figure out how to convert my data
>>> to the required format; the explanation of the arrayspecs routine in the
>>> "Quick Guide to Geomorph" was not clear for me (and it lacks a workin
>>> exemple).
>>>
>>>  My data are read from a NTSYSpc file containing 2D coordinates for 10
>>> landmarks for a number of fish specimens, using the readland.nts routine. I
>>> have been able to perform a PCA on these data using the shapepca routine in
>>> Ian Dryden's shapes R package, but would like to perfom the entire analysis
>>> using geomorph.
>>>
>>>  Thanks in advance for any hints!
>>>
>>>  Best regards,
>>>
>>> --
>>> Dr. Mauro J. Cavalcanti
>>> E-mail: mauro...@gmail.com
>>> Web: maurobio 
>>>
>>>  --
>>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>>>
>>>  To unsubscribe from this group and stop receiving emails from it, send
>>> an email to morphmet+unsubscr...@morphometrics.org.
>>>
>>
>>
>> --
>>
>> ~~~
>>
>> Emma Sherratt, PhD.
>>
>> Lecturer in Zoology,
>> Zoology Division, School of Environmental and Rural Science,
>> Room L120 Bldg C02,
>> University of New England,
>> Armidale, NSW, Australia, 2351
>> Tel: +61 2 6773 5041
>> email: emma.sherr...@une.edu.au
>> Twitter: @DrEmSherratt
>>
>>  Caecilians are legless amphibians...
>>
>> *  __
>> (\   .-.   .-.   /_")
>>  \\_//^\\_//^\\_//
>>   `"`   `"`   `"`*
>>
>> learn more about them here: www.emmasherratt.com/caecilians
>>
>>
>>
>>
>>
>
>
> --
> Dr. Mauro J. Cavalcanti
> E-mail: mauro...@gmail.com
> Web: http://sites.google.com/site/maurobio
>
>  --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
>  To unsubscribe from this group and stop receiving emails from it, send
> an email to morphmet+unsubscr...