[adegenet-forum] DAPC and coordinates

[Jombart, Thibaut]

Hi Bernhard, 

what are the error messages you received? To try and find the problem, you can try to plot the spatial coordinates separately to make sure everything's OK. For instance:
plot(xy)

Also compare the dimensions of the two objects:
dim(xy)
dim(dapc1$grp.coord)

If the number of rows differ, this is a problem. I will be travelling the next week, so sorry if I don't reply soon.

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 Bernhard Stoeckle (Wildbiologie) [stoeckle at wzw.tum.de]
Sent: 02 December 2010 08:49
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] DAPC and coordinates

Dear Thibaut,


thank you very much for your last answer. It worked perfect! I am really sorry
but I have one last question and I would be glad if you can help me again.
I have a microsatellite data set (8 populations and 12 loci) with geographical coordinates and I made a
dapc and it worked well. Then I tried to visualize the dapc in combination with the
geographical coordinates and it failed. I did the following:

I loaded also the package "maps" and I created a textfile named popInfo and it
looked like this:

Population,Longitude,Latitude
1,48.150341,11.881521
2,48.149266,11.887157
3,48.147861,11.874697
4,48.143326,11.973001
5,48.147606,11.899779
6,48.101255,11.870512
7,48.162266,11.970248
8,48.127254,11.915180


Then I tried to visualize the dapc results according
to the example eHDGP in the manual with the following commands:


> xy <- cbind(grp$other$popInfo$Longitude, grp$other$popInfo$Latitude)
> par(mar=rep(.1,4))
> map(fill=TRUE, col="lightgrey")
> colorplot(xy, -dapc1$grp.coord, cex=3, add=TRUE, trans=FALSE)



But it did not work. R showed a couple of error messages.
I would be glad if you can help me again.


Bernhard


Technische Universitaet Muenchen TUM
Lehrstuhl für Zoologie
AG Molekulare Zoologie
Hans-Carl-von-Carlowitz-Platz 2
85354 Freising