include ellipse to plot_ordination

[locon833]

Is there a command to add ellipse around cluster in your NMDS or PCoA plots?

x1=plot_ordination(sponge.scale1,unifrac.nmds,color="Day")+geom_point(size=3)

I tried following:
https://www.biostars.org/p/126454/

but hit a roadblock at
ord = ordinate(GP1~Day, "CCA", "bray")
Error in eval(expr, envir, enclos) : object 'Day' not found
In addition: Warning message:
First argument, physeq, as formula is deprecated.
There is now an explicit formula argument.
Please revise method call accordingly.

[joey711]

I'll add this very soon...

[spholmes]

Joey
If you look at the code in the paper I wrote with Sue Huse and Ana on
prevotella and lifestyle in microbiome, there are several ellipse examples
to go on.

I used the ellipse package

Susan

On Mon, May 16, 2016 at 9:34 AM, Paul J. McMurdie [email protected]
wrote:

I'll add this very soon...

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#58 (comment)

Susan Holmes
Professor, Statistics and BioX
John Henry Samter Fellow in Undergraduate Education
Sequoia Hall,
390 Serra Mall
Stanford, CA 94305
http://www-stat.stanford.edu/~susan/

[joey711]

Thanks @spholmes ! Actually, ellipses are finally natively supported in ggplot2, so I was simply going to add an ellipse layer. I think it takes function inputs as alternative ellipse definitions. If so, I may peak at your examples and the ellipse package to expose those alternatives.

Right now I'm a bit distracted adding the plotly/D3 interactive versions, on a separate branch ftm. I should add this to that branch as a working demo before pushing into the master.

[orenkolodny]

Have ellipses been added, by any chance? I don't see anything in the documentation.
Thanks!
Oren