[adegenet-forum] polyploids sPCA plot failure

[Chad Smith]

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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