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should we flag new users about problems with possible colinearity issues if their metadata categories are too similar (e.g. including a continuous value of BMI and a quartile category of BMI)?
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https://github.com/biocore/DEICODE/blob/0d480ced82fcc28df3a0fd554ae06513cb0e9d4f/deicode/rpca.py#L62-L71
DEICODE currently adds a PC3 of zeroes if rank is 2, due to an old Emperor bug. This results…
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From private e-mail:
CA, MCA, PCA, MDS (ExPosition, InPosition for inferences)
Discriminant Correspondence Analysis (DiCA), PLSC, (TExPosition, TInPosition for inferences), barycentrique discrim…
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Hi Shuangbin,
I'm wondering how to set the aesthetic mapping of PCoA use the _mapping_ parameter in the _ggordpoint_ function. It seems to be that I can change the shape, size, or alpha of the p…
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First, I want to thank for making such a great package for multivariate and ecological community analyses! I use vegan a lot in my work. One thing I constantly miss is the possibility to quickly glanc…
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### Background
I am trying to put together a biplot plotter based on the results of `stat.PC`, but it's harder than it needs to be, with it being necessary to re-center the data even though this …
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Used to have these in the package and at some point removed them but now think they should be back
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Would be great to have the loadings associated with each OTU from a PCoA to better explore the taxonomic differences between samples/treatments. This can also be done by comparing OTU abundances with…
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We want to support [Principle Component Analysis](https://en.wikipedia.org/wiki/Principal_component_analysis) as an advanced analytics option.
For an intro to PCA and how it looks in R it's worth l…
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Hi Joey,
I have a microbial dataset with taxa (species) and samples and I'm plotting these in a PCoA based on Bray-Curtis. Based on the PERMANOVA, I selected 20 taxa out of >5600 that are most import…