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<p class="MsoNormal">Hello all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m attempting to recreate a similar figure to the one seen in Sarno et al. (<a href="http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0096074&representation=PDF">http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0096074&representation=PDF</a>).
To do so, I create the attached matrix (HGF.txt) that contains populations (rows) and Y-STR haplogroups (columns). Additionally, due to my inexperience with adegenet, I created the attached coordinates list in a separate file (XY.txt). I then did the following.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Function:<o:p></o:p></p>
<pre style="word-break:break-all">mydata <- <span style="font-family:"Lucida Console";color:blue;background:#E1E2E5">genpop(HGF,ploidy=1)</span><span style="font-family:"Lucida Console";color:black;background:#E1E2E5"><o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Result:<o:p></o:p></p>
<p class="MsoNormal">Object created<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Function:<o:p></o:p></p>
<pre style="word-break:break-all"><span class="gcg2ujhdeab"><span style="font-family:"Lucida Console";color:blue;background:#E1E2E5">spca(mydata,xy=xy,d1=0,d2=5)</span></span><span style="font-family:"Lucida Console";color:black;background:#E1E2E5"><o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Result:<o:p></o:p></p>
<p class="MsoNormal">Plot created<o:p></o:p></p>
<p class="MsoNormal"><img border="0" width="306" height="130" id="Picture_x0020_1" src="cid:image003.jpg@01D0B4E0.1EA1AB50"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Now comes the problem. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Function:<o:p></o:p></p>
<pre style="word-break:break-all"><span class="gcg2ujhdeab"><span style="font-family:"Lucida Console";color:blue;background:#E1E2E5">myspca<-spca(mydata,xy=xy,type=5,d1=0,d2=5)</span></span><span style="font-family:"Lucida Console";color:black;background:#E1E2E5"><o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Result:<o:p></o:p></p>
<p class="MsoNormal">No “myspca” list is created and I get the following error<o:p></o:p></p>
<pre style="word-break:break-all"><span class="gcg2ujhdiab"><span style="font-family:"Lucida Console";color:#C5060B;background:#E1E2E5">Error in if (nf > rank) nf <- rank : <o:p></o:p></span></span></pre>
<pre style="word-break:break-all"><span class="gcg2ujhdiab"><span style="font-family:"Lucida Console";color:#C5060B;background:#E1E2E5"> missing value where TRUE/FALSE needed</span></span><span style="font-family:"Lucida Console";color:black;background:#E1E2E5"><o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I feel that if I can obtain the eig values for the dataset the rest will be smooth sailing; however, I am unable to find any similar instances on the forum (some people have mentioned this general error in regard to clustering but not spca).
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help is greatly appreciated. Thanks in advance <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Jonathan King</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Research and Development Lab Manager</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Institute of Applied Genetics</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">UNT Health Science Center</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">3500 Camp Bowie Blvd</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Fort Worth, TX 76107</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Office: 817-735-2773<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Phone: 817-735-2940</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://www.unthsc.edu/graduate-school-of-biomedical-sciences/molecular-and-medical-genetics/laboratory-faculty-and-staff/">Research and Development Lab</a><u><span style="color:blue"><o:p></o:p></span></u></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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