Great!!! Thanks!!!<br clear="all">-------------<br>Consuelo Hermosilla<br>PhD student<br>Departamento de Ecología y Biología Animal<br>Departamento de Bioquímica, Genética e Inmunología, Área de Genética<br>Facultad de Ciencias del Mar<br>
Campus de As Lagoas-Marcosende<br>Universidad de Vigo<br>36310 Vigo<br>SPAIN<br>Mobile: +34 692 633 298<br><br>oooO<br>( ) Oooo<br> ( ( )<br> _) ) /<br> (_/<br><br>Stop Gaza Massacre<br>
<br><br><div class="gmail_quote">On Wed, Apr 21, 2010 at 11:40 AM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Consuelo,<br>
<br>
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.<br>
<br>
As for the plot:<br>
##########<br>
## uses example from the doc:<br>
load(system.file("files/mondata1.rda",package="adegenet"))<br>
cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE)<br>
mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2)<br>
plot(mon1,mondata1$x1)<br>
<br>
## to add a title<br>
title("my title")<br>
<br>
## to add text on the locations<br>
par(xpd=TRUE)<br>
text(mondata1$xy[,1], mondata1$xy[,2], 1:70, col="red")<br>
##########<br>
<br>
Best<br>
<br>
Thibaut.<br>
________________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] On Behalf Of Consuelo Hermosilla [<a href="mailto:cheluna@gmail.com">cheluna@gmail.com</a>]<br>
Sent: 20 April 2010 15:31<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] monmonier<br>
<div><div></div><div class="h5"><br>
Hi Thibaut,<br>
<br>
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! :)<br>
<br>
Thanks!!<br>
<br>
Consuelo<br>
<br>
-------------<br>
Consuelo Hermosilla<br>
PhD student<br>
Departamento de Ecología y Biología Animal<br>
Departamento de Bioquímica, Genética e Inmunología, Área de Genética<br>
Facultad de Ciencias del Mar<br>
Campus de As Lagoas-Marcosende<br>
Universidad de Vigo<br>
36310 Vigo<br>
SPAIN<br>
Mobile: +34 692 633 298<br>
<br>
oooO<br>
( ) Oooo<br>
( ( )<br>
_) ) /<br>
(_/<br>
<br>
Stop Gaza Massacre<br>
</div></div></blockquote></div><br>