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erikrikarddaniel / pf-gtdb-analyses

Analysis tools for Pfitmap/RNRdb/GTDB
MIT License
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NrdR Anvi'o table (and more?) in separate script #8

Open erikrikarddaniel opened 4 years ago

erikrikarddaniel commented 4 years ago

The data needed by the Anvi'o visualisations should not be created by NrdR.Rmd but by a separate script (in scripts/, e.g. scripts/nrdr_anvio.R). There are two consequences I'm not totally sure about:

  1. I think we should call this script from the build process, i.e. make all in data. The output will hence be in data/. We should possibly have a subdirectory for this... Another option would be to have a different directory structures for analysis specific tables with make targets for the various analyses.

  2. It's possible that the above script should be more general and do all the lifting that is now done in the Rmd to create the nrdrs and rnrs tables.

erikrikarddaniel commented 4 years ago

I started the Rmd parts of this in scripts/rnr_convenience_tables.R (called by all in data/Makefile) 3d7d49304ec51bfe2d4f5e49ea7dc82e245679ef. Only output as feather for now.