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rprops / Phenoflow_package

R package offering functionality for the advanced analysis of microbial flow cytometry data
GNU General Public License v2.0
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Leinster & Cobbold implementation #27

Closed FMKerckhof closed 6 years ago

FMKerckhof commented 7 years ago

A similarity-sensitive diversity metric may be of added value. Phyloseq's data structure allows including a phylogenetic tree within the object, which should be relatively eassy to extract distance information from. However, the question remains: how would you make a similarity-sensitive metric on flowcytometric fingerprint data?

FMKerckhof commented 7 years ago

Alternatively, we could let the user provide any distance matrix of their choice to Diversity_16S

rprops commented 7 years ago

Would need to check formula for calculating the similarity based diversity metrics but should be fairly straightforward to implement, I think

rprops commented 7 years ago

Started working on it.

FMKerckhof commented 7 years ago

I wouldn't mind doing this in lieu of you, but I am only available from the 2nd of Feb on.

rprops commented 7 years ago

Sure you can go for it - I'm curious. I'm afraid the computation of those indices will take a lot of time, due to the size of the expected dissimilarity matrix.

FMKerckhof commented 7 years ago

would there be a heuristic approach?

FMKerckhof commented 6 years ago

@rprops what about using the Mahalanobis distance? Or is it too sensitive to the number of selected parameters?

rprops commented 6 years ago

Not possible (for now) to include in Phenoflow given the type of data we get from FCM.