[adegenet-forum] monmonier

[Consuelo Hermosilla]

Great!!! Thanks!!!
-------------
Consuelo Hermosilla
PhD student
Departamento de Ecología y Biología Animal
Departamento de Bioquímica, Genética e Inmunología, Área de Genética
Facultad de Ciencias del Mar
Campus de As Lagoas-Marcosende
Universidad de Vigo
36310 Vigo
SPAIN
Mobile: +34 692 633 298

oooO
(     ) Oooo
   (   (     )
  _)    )  /
        (_/

Stop Gaza Massacre


On Wed, Apr 21, 2010 at 11:40 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk
> wrote:

> Dear Consuelo,
>
> in Monmonier's algorithm, we seek a path (a boundary) which shows the
> largest differences between pairs of neighbors. Differences are measured by
> a genetic distance (in the case of genetic data). If the distance is too
> faint, then chances are that there is no longer a 'boundary', and then the
> path should stop. The argument 'threshold' is used to specify this distance
> at which to stop the path. If it is "1.123", then the path will cross only
> differences between neighbours greater than 1.123.
>
> As for the plot:
> ##########
> ## uses example from the doc:
> load(system.file("files/mondata1.rda",package="adegenet"))
> cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE)
> mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2)
> plot(mon1,mondata1$x1)
>
> ## to add a title
> title("my title")
>
> ## to add text on the locations
> par(xpd=TRUE)
> text(mondata1$xy[,1], mondata1$xy[,2], 1:70, col="red")
> ##########
>
> Best
>
> Thibaut.
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Consuelo
> Hermosilla [cheluna at gmail.com]
> Sent: 20 April 2010 15:31
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] monmonier
>
> Hi Thibaut,
>
> I'm trying to use the monmonier function, but I don't understand very well
> the threshold argument. Can you explain it more in detail? Another issue, is
> it possible to add the populations names to the monmonier plot? Because if I
> try the text function, it doesn't insert anything... the main option didn't
> work either... is this normal? Sorry, I don't mean to complain, I think you
> work is great! I just want to know if it can be done! :)
>
> Thanks!!
>
> Consuelo
>
> -------------
> Consuelo Hermosilla
> PhD student
> Departamento de Ecología y Biología Animal
> Departamento de Bioquímica, Genética e Inmunología, Área de Genética
> Facultad de Ciencias del Mar
> Campus de As Lagoas-Marcosende
> Universidad de Vigo
> 36310 Vigo
> SPAIN
> Mobile: +34 692 633 298
>
> oooO
> (     ) Oooo
>   (   (     )
>  _)    )  /
>        (_/
>
> Stop Gaza Massacre
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20100421/fa070303/attachment.htm