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EcoJulia / Microbiome.jl

For analysis of microbiome and microbial community data
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vignette for data import #112

Closed aguang closed 2 years ago

aguang commented 2 years ago

A vignette describing how to create CommunityProfile objects from imported CSVs would be helpful. The JOSS preprint says that it is trivial to go from .csv files to CommunityProfile and vice versa, but I did not find that to be the case. It wasn't extremely difficult, but I did have to convert my row names to a Taxon vector, my column names to a MicrobiomeSample vector, and my matrix to a SparseMatrixCSC object. If there is an easier way to do it then I would love to know and have that be in the documentation.

kescobo commented 2 years ago

You're right - that's the process :grimacing: ... I guess easy is relative here.

I wonder if a constructor like

communityprofile(t; featurecontructor)

Where t is a table and featureconstructor is a function that would be applied to the first column would be worth adding...