[adegenet-forum] customize labels within centroid

[Jombart, Thibaut]

Hello, 

Just to clarify, R uses no 'file' for storing objects during a session, everything is stored in the RAM.

The rule in R is to type the name of an object to print its content. You can use '@' or '$' to access the content of genind objects.
In your case, you're looking for:
##
H3N2 at other$epid
##

which is simply a vector of numeric. You can pass any vector of character, numeric, or factor to 'pop' to change the population information of a genind. The only requirement is for this vector to have a length which is the number of individuals in the study.

Cheers

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 J. Richardson [jrichardson4 at gmail.com]
Sent: 12 November 2012 21:05
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] customize labels within centroid

Hi Thibaut and Adegenet users,

I have what I think is a simple/quick question, but have not been able to figure out on my own or via the archives. I have a dataset (Genepop formatted) I have been working with to conduct DAPC and create a scatterplot. I have a legend with each population/sampling site name listed (there are 13), which roughly corresponds to the population/site names within the Genepop file (between each "POP" line). I would like to include these same labels within each of the 13 centroids on the scatterplot, but currently when I set "clab=1" the labels are displayed "P01", "P02"... "P13" rather than the names of the populations/sites in the data file or the object created to put this names in the legend.

Do you know how I can change these labels, either manually with a new object for the "clab=" command to use, or for "scatter" to refer to in the Genepop input file? I see in the H3N2 example, that the labels were amended to the epidemic years - I think using the "pop(H3N2) <- H3N2$other$epid" line. But I can't figure out how to display the H3N2 data to see how the "epid" item is incorporated into the file.

Thank you in advance for any advice or insights.

Jonathan