[adegenet-forum] polyploids sPCA plot failure

[Roman Luštrik]

Can you make this reproducible and post it to github (https://github.com/thibautjombart/adegenet/issues)? 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Chad Smith" <chadsmith at utexas.edu> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Monday, January 30, 2017 4:39:41 PM 
Subject: [adegenet-forum] polyploids sPCA plot failure 

I have a polyploid data set with different ploidy levels for different individuals. 

When plotting the spca object I get "arguments imply differing number of rows" and a multispati "There are only 21 positive factors" error. The eigenvalues decomposition plot does not appear. 

Please advise on how to troubleshoot this problem. There were no errors creating the sPCA object. Thanks! 

> atm1.spca.2 
######################################## 
# spatial Principal Component Analysis # 
######################################## 
class: spca 
$call: spca(obj = obj, type = 2) 

$nfposi: 3 axis-components saved 
$nfnega: 4 axis-components saved 
Positive eigenvalues: 0.136 0.0168 0.014 0.0101 0.00731 ... 
Negative eigenvalues: -0.00324 -0.0021 -0.0016 -0.00143 -0.000756 ... 

vector length mode content 
1 $eig 39 numeric eigenvalues 

data.frame nrow ncol content 
1 $c1 79 7 principal axes: scaled vectors of alleles loadings 
2 $li 118 7 principal components: coordinates of entities ('scores') 
3 $ls 118 7 lag vector of principal components 
4 $as 2 7 pca axes onto spca axes 

$xy: matrix of spatial coordinates 
$lw: a list of spatial weights (class 'listw') 

other elements: NULL 
> plot(atm1.spca.2) 
Error in data.frame(eig = eig, var = varspa, moran = moran/varspa) : 
arguments imply differing number of rows: 39, 38 
In addition: Warning message: 
In multispati(dudi = dudi, listw = lw, scannf = FALSE, nfposi = nfposimax, : 
There are only 21 positive factors. 
> 

Cheers, 
Chad 

-- 
Chad Smith 
Postdoctoral Fellow 
Dept of Integrative Biology 
University of Texas at Austin 
1 University Station C0990 
Austin, TX 78712 

Office: PAT 632 
Phone: 512-471-7619 
Fax: 512-471-3878 
https://chadcsmith.wordpress.com/ 

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