[adegenet-forum] Loading plots and sPCA scores

[Jombart, Thibaut]

Dear Roy, 

> Firstly, for a normal PCA (dudi.pca), is it possible to see the contribution of alleles/loci to the first PC?

$c1; please see the doc (vignette("adegenet-basics"), p.42-43).

> Secondly, in sPCA, what is the difference between the actual scores (myspca$li) and lagged scores (myspca$ls)?

Let 'x' be the vector of a given principal component (or any real-valued vector in) and W be a matrix of spatial weights. The line "i" of W contains spatial weights defining proximities of all locations to location "i". Then, the lag vector 'y' is simply given by 'y=Wx'.

That is, any value at a given location is replaced by the average value computed on neighbouring locations. Maps of lagged variables are thus smoothed, sometimes allowing to clarify spatial structures.

Cheers

Thibaut.

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Roy Francis Mathew [RoyFrancis.Mathew at agrsci.dk]
Sent: 05 September 2011 12:01
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: Re: [adegenet-forum] Loading plots and sPCA scores

Hi,
I have two questions.
Firstly, for a normal PCA (dudi.pca), is it possible to see the contribution of alleles/loci to the first PC?
I have seen something similar in sPCA called the loading plot and it looks nice.

Secondly, in sPCA, what is the difference between the actual scores (myspca$li) and lagged scores (myspca$ls)?

Kind regards
Roy Mathew Francis

Dept. of Integrated Pest Management
Aarhus University
Forsøgsvej 1
DK-4200 Slagelse


Tel.: +45
Email: RoyFrancis.Mathew at agrsci.dk


Tel.: +45 8999 1900
Web: www.agrsci.au.dk

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