<html><body><div style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000"><div>Can you make this reproducible and post it to github (https://github.com/thibautjombart/adegenet/issues)?</div><div><br data-mce-bogus="1"></div><div>Cheers,</div><div>Roman</div><div><br></div><div data-marker="__SIG_PRE__">----<br>In god we trust, all others bring data.</div><br><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>From: </b>"Chad Smith" <chadsmith@utexas.edu><br><b>To: </b>adegenet-forum@lists.r-forge.r-project.org<br><b>Sent: </b>Monday, January 30, 2017 4:39:41 PM<br><b>Subject: </b>[adegenet-forum] polyploids sPCA plot failure<br></div><br><div data-marker="__QUOTED_TEXT__"><div dir="ltr"><div><div>I have a polyploid data set with different ploidy levels for different individuals.<br><br></div>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. <br><br></div>Please advise on how to troubleshoot this problem. There were no errors creating the sPCA object. Thanks! <br><div><div><br>> atm1.spca.2<br> ########################################<br> # spatial Principal Component Analysis #<br> ########################################<br>class: spca<br>$call: spca(obj = obj, type = 2)<br><br>$nfposi: 3 axis-components saved<br>$nfnega: 4 axis-components saved<br>Positive eigenvalues: 0.136 0.0168 0.014 0.0101 0.00731 ...<br>Negative eigenvalues: -0.00324 -0.0021 -0.0016 -0.00143 -0.000756 ...<br><br> vector length mode content <br>1 $eig 39 numeric eigenvalues<br><br> data.frame nrow ncol content <br>1 $c1 79 7 principal axes: scaled vectors of alleles loadings <br>2 $li 118 7 principal components: coordinates of entities ('scores')<br>3 $ls 118 7 lag vector of principal components <br>4 $as 2 7 pca axes onto spca axes <br><br>$xy: matrix of spatial coordinates<br>$lw: a list of spatial weights (class 'listw')<br><br>other elements: NULL<br>> plot(atm1.spca.2)<br>Error in data.frame(eig = eig, var = varspa, moran = moran/varspa) : <br> arguments imply differing number of rows: 39, 38<br>In addition: Warning message:<br>In multispati(dudi = dudi, listw = lw, scannf = FALSE, nfposi = nfposimax, :<br> There are only 21 positive factors.<br>> <br><br><div>Cheers,<br></div><div>Chad<br clear="all"></div><div><div><br>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Chad Smith<div>Postdoctoral Fellow</div><div>Dept of Integrative Biology</div><div>University of Texas at Austin</div><div>1 University Station C0990</div><div>Austin, TX 78712</div><br><div>Office: PAT 632</div><div>Phone: 512-471-7619</div><div>Fax: 512-471-3878</div><div><a href="https://chadcsmith.wordpress.com/" target="_blank">https://chadcsmith.wordpress.com/</a></div></div></div></div></div></div></div>
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