[adegenet-forum] DAPC axes

[Thibaut Jombart]

Re the grid: it was a choice in the plotting design of ade4 to display the
mesh of the grid at the top right corner of the graph, rather than
annotations + tick marks. You can always make custom graphs e.g. using
ggplot2.

Best of luck in your analyses

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 11:43, Said D. <said_wali at hotmail.com> wrote:

> Dear Thibaut, dear Cathy,
> thank you for the quick reply.
> Now it is clear to me.
> With respect to "grid = TRUE", it is only showing the grid but not the
> labels of the axis ticks.
> Till now I was not able to find it.
> Thank you.
> Said
>
>
>
> ------------------------------
> *Von:* Thibaut Jombart <thibautjombart at gmail.com>
> *Gesendet:* Mittwoch, 30. September 2020 11:21
> *An:* Said D. <said_wali at hotmail.com>
> *Cc:* adegenet-forum at lists.r-forge.r-project.org <
> adegenet-forum at lists.r-forge.r-project.org>
> *Betreff:* Re: [adegenet-forum] DAPC axes
>
> 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://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Frepidemicsconsortium.org%2F&data=02%7C01%7C%7Ca0a7b1e41e334029916408d8652242c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637370545101710587&sdata=xyxXby9GkiXy6wBmradI%2FVXo2WR%2BOUezlxmjpn5izOs%3D&reserved=0>
> https://thibautjombart.netlify.com
> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fthibautjombart.netlify.com%2F&data=02%7C01%7C%7Ca0a7b1e41e334029916408d8652242c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637370545101720582&sdata=RAdao75S9fxedpxovHHjFhGZ0glSKI90KUDw1zcDA70%3D&reserved=0>
> 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
> <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>
>
> It is also a pity that the original DAPC scatter plot is not showing the
> scale.
> Thank you.
> Said
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.r-forge.r-project.org%2Fcgi-bin%2Fmailman%2Flistinfo%2Fadegenet-forum&data=02%7C01%7C%7Ca0a7b1e41e334029916408d8652242c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637370545101730576&sdata=f3uCuMYRPRi9XtlSqNO%2BvrZ7imIPKE2BSlwrGN%2BZKRU%3D&reserved=0>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200930/246a6234/attachment-0001.html>