[adegenet-forum] DAPC axes

[Thibaut Jombart]

Dear Said,

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.

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.

Best
Thibaut

--
Dr Thibaut Jombart
Associate Professor in Outbreak Analytics, London School of Hygiene and
Tropical Medicine
Senior Lecturer in Genetic Analysis, Imperial College London
UK Public Health Rapid Support Team
President of RECON: repidemicsconsortium.org
https://thibautjombart.netlify.com
Twitter: @TeebzR


On Wed, 30 Sep 2020 at 09:29, Said D. <said_wali at hotmail.com> wrote:

> Hi everyone,
> 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.
> Should I call them PC1 and PC2 or LD1 and LD2?
> Here they call the axes LD1 and LD2
> https://grunwaldlab.github.io/Population_Genetics_in_R/clustering_plot.html
>
> It is also a pity that the original DAPC scatter plot is not showing the
> scale.
> Thank you.
> Said
>
>
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