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vegan::capscale ordination in phyloseq #312

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iLivius opened this Issue Mar 17, 2014 · 5 comments

2 participants

@iLivius
iLivius commented Mar 17, 2014

Dear Dr. McMurdie,

I’m currently into microbial community analysis and an eager user of your package. Big fan!
We just got a paper accepted in PLOS ONE (about endophyte bugs in grapevines after several treatments, classic microbial ecology study, 16S rRNA pyroseqs) but still one reviewer made mincemeat out of me since I used a CCA for constraining variables. I would like to use then a Constrained Analysis of Principal Coordinates (CAP), since I’ve already used its PCoA counterpart as an unconstrained approach early in the analysis.

I’m almost sure that the vegan::capscale (http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/capscale.html) is not wrapped into phyloseq. Can you please suggest me how should I use that function as an ordination in phyloseq?

Thank you very much in advance

Cheers
Livio

@joey711 joey711 added the Feature label Mar 18, 2014
@joey711
Owner
joey711 commented Mar 18, 2014

This is an feature request that I will look into. Thanks for your interest!

joey

@joey711
Owner
joey711 commented Mar 24, 2014

This won't be difficult to include. I've partially completed. I'll test it and post an example here when I post the update.

@joey711 joey711 added a commit that referenced this issue Mar 26, 2014
@joey711 1.7.24 Support for CAP. Revised `ordinate`, added `formula` argument.…
… Additional ord unit tests.

CHANGES IN VERSION 1.7.24
-------------------------

USER-VISIBLE CHANGES

	- Added support for [Partial] Constrained Analysis of Principal
Coordinates (CAP).

		- A supported/documented option in `ordinate`, supported by
`plot_ordination`.

		- This solves [Issue
312](#312).

	- The `ordinate` function now takes an explicit `formula` argument.

		- This facilitates reliable contrained ordination calls for:

			- CAP (this commit)

			- RDA (partial redundancy analysis)

			- CCA (constrained correspondence analysis)
1b20634
@joey711
Owner
joey711 commented Mar 26, 2014

This is also a specific case of the broader issue I suggested for supporting further ordination result classes (indicating other PCA classes as an example) in the following:

#218

@joey711
Owner
joey711 commented Mar 27, 2014

Done. See the "CAP" option in the ordinate function after updating your phyloseq version to 1.7.24+.

Thanks for the feedback. Always helpful.

joey

@joey711 joey711 closed this Mar 27, 2014
@iLivius
iLivius commented Mar 27, 2014

Just got my data tested with the brand new 1.7.24 version. The ordinate() function is more powerful than ever, working like a charm!

Thank you so much, big fan

Livio

@joey711 joey711 was assigned by iLivius Mar 27, 2014
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