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Dear Thibaut, dear Cathy,</div>

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thank you for the quick reply. </div>

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Now it is clear to me. <br>

With respect to "<span style="color: rgb(0, 0, 0); font-family: "trebuchet ms", sans-serif; font-size: 15px; background-color: rgb(255, 255, 255); display: inline !important;">grid = TRUE", it is only showing the grid but not the labels of the axis ticks.</span></div>

<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><font face="trebuchet ms, sans-serif"><span style="font-size: 15px;">Till now I was not able to find it.</span></font></div>

<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><font face="trebuchet ms, sans-serif"><span style="font-size: 15px;">Thank you.<br>

Said</span></font></div>

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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Von:</b> Thibaut Jombart <thibautjombart@gmail.com><br>

<b>Gesendet:</b> Mittwoch, 30. September 2020 11:21<br>

<b>An:</b> Said D. <said_wali@hotmail.com><br>

<b>Cc:</b> adegenet-forum@lists.r-forge.r-project.org <adegenet-forum@lists.r-forge.r-project.org><br>

<b>Betreff:</b> Re: [adegenet-forum] DAPC axes</font>

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<div class="x_gmail_default" style="font-family:trebuchet ms,sans-serif">Dear Said, </div>

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<div class="x_gmail_default" style="font-family:trebuchet ms,sans-serif">both terminologies are correct: LDs are merely PCs of a discriminant analysis. But as DAPC has 2 sets of PCs, one of the initial PCA, then one for the follow-up discriminant analysis,

 LDs will be less ambiguous. </div>

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<div class="x_gmail_default" style="font-family:trebuchet ms,sans-serif">As for the scale on scatterplots of DAPC: it is disabled by default as not usually used, but you can add a grid using grid = TRUE. See ?scatter.dapc for further options.</div>

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<div class="x_gmail_default" style="font-family:trebuchet ms,sans-serif">Best</div>

<div class="x_gmail_default" style="font-family:trebuchet ms,sans-serif">Thibaut</div>

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<div><font face="arial, helvetica, sans-serif">--<br>

Dr Thibaut Jombart<br>

Associate Professor in Outbreak Analytics, London School of Hygiene and Tropical Medicine<br>

Senior Lecturer in Genetic Analysis, Imperial College London</font></div>

<div><font face="arial, helvetica, sans-serif">UK Public Health Rapid Support Team</font></div>

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<div dir="ltr" class="x_gmail_attr">On Wed, 30 Sep 2020 at 09:29, Said D. <<a href="mailto:said_wali@hotmail.com">said_wali@hotmail.com</a>> wrote:<br>

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Hi everyone,</div>

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I googled a lot (Maybe I was not lucky enough) but I could not find a real explanation out the axes of the DAPC scatter plot.</div>

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Should I call them PC1 and PC2 or LD1 and LD2?</div>

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Here they call the axes LD1 and LD2</div>

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<a href="https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgrunwaldlab.github.io%2FPopulation_Genetics_in_R%2Fclustering_plot.html&data=02%7C01%7C%7Ca0a7b1e41e334029916408d8652242c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637370545101720582&sdata=ott8hyt8zedQ1OGkSD80DV3tbjjxg55q%2BVyLXs0G%2BMA%3D&reserved=0" originalsrc="https://grunwaldlab.github.io/Population_Genetics_in_R/clustering_plot.html" shash="Kjw7QvmJHgmKk8jSvf+oIsiVDaW63NzlLsUrf7g3Qeeh/FVeqPQ8vhTlTUiUnVW0fXiLYBgUN1/CKwjUTs7b+6JDah7Ur6S6/KgcIeDGwh82kL+WTJCsig1H9f6IrVaw1N7ZBQK3z1CFKeU9LtuLCBzSbfe1PWXnxqfOzbzHkMs=" id="x_gmail-m_-3703493816954147254LPlnk708253" target="_blank">https://grunwaldlab.github.io/Population_Genetics_in_R/clustering_plot.html</a><br>

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It is also a pity that the original DAPC scatter plot is not showing the scale.</div>

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Thank you.<br>

Said</div>

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