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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font size="2">Hi there,
<br>
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1) It is the plot of two principal components of the analysis (by default x=1 and y=2), i.e. the synthetic variables best discriminating your groups (in the sense of the ratio of variance between group / within group)<br>
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2) It is exactly what it reads on the box, i.e. a one dimensional representation of the chosen principal component (typically the first and only one); tick marks are individuals, and the density curves are derived by kernel density estimation, i.e.: they show
you where individuals are.<br>
<br>
The phrase:<br>
"</font><font size="2">proportion of individuals in groups against the eigenvalues of the first discriminant function"<br>
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<div class="PlainText">does not really make sense I'm afraid ;) It may be useful to check the paper, if you have not yet, hopefully this would bring some clarifications (apologies if not).<br>
<br>
Best<br>
Thibaut<br>
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<div style="direction: ltr;" id="divRpF419551"><font color="#000000" face="Tahoma" size="2"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of kin onn [kin_onn@yahoo.com]<br>
<b>Sent:</b> 01 October 2015 19:11<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] interpreting scatter plot from dapc analysis<br>
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<div id="yui_3_16_0_1_1443722265378_3660">Dear all,</div>
<div id="yui_3_16_0_1_1443722265378_3667"><br>
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<div id="yui_3_16_0_1_1443722265378_3668">I have a question regarding the interpretation of two types of scatter plots from the dapc analysis </div>
<div id="yui_3_16_0_1_1443722265378_3819" dir="ltr">1) the cluster plot from the function scatter(dapc1). The axes are not labeled and I was wondering what they were</div>
<div id="yui_3_16_0_1_1443722265378_3883" dir="ltr">2) the scatter that represents a single discriminant function from the function scatter(dapc1,1,1). In the tutorial it says that it plots the density of individuals against the discriminant function. Is this
the proportion of individuals in groups against the eigenvalues of the first discriminant function? How should we interpret this graph?</div>
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<div dir="ltr">Thank you in advance!</div>
<div id="yui_3_16_0_1_1443722265378_3669"><br>
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<div id="yui_3_16_0_1_1443722265378_3670"><br>
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<div class="signature" id="yui_3_16_0_1_1443722265378_3672">Best regards,
<div id="yui_3_16_0_1_1443722265378_3678">Chan </div>
<div id="yui_3_16_0_1_1443722265378_3671">Biodiversity Institute and Department of Ecology and Evolutionary Biology </div>
<div id="yui_3_16_0_1_1443722265378_3673">University of Kansas </div>
<div id="yui_3_16_0_1_1443722265378_3677">Dyche Hall, 1345 Jayhawk Blvd </div>
<div id="yui_3_16_0_1_1443722265378_3676">Lawrence, KS 66045-7593</div>
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