[adegenet-forum] monmonier

[Jombart, Thibaut]

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

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