statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
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Implement "show correlated phenotypes" feature on pheno page #123

Closed abought closed 4 years ago

abought commented 5 years ago

Purpose

Per @sgagliano / @dtaliun request, implements a "show correlated phenotypes" table on the phenotype summary page, under the manhattan/ QQ plot.

screen shot 2019-03-05 at 4 47 20 pm

Design notes

The design spec calls for this to be an optional feature. The basic ingest step (pheweb process) will warn if the correlation file is missing, but only fail if the feature has been explicitly requested (via the config file). This new piece of data can be incrementally added to an existing pheweb by running a single new command. (see below)

The rg pipeline file format is still being worked out, and the current iteration is not very tolerant of file format inconsistencies. Eventually we may want to incorporate the pipeline directly into Pheweb, to ensure more consistent data processing.

How to test this

(TODO: add test data!)

The below instructions should reflect what has been added to README.md.

The correlation file can be incorporated by copying pheno-correlations.txt into the same folder as pheno-list.json, and then running the new subcommand:

$ phweb pheno-correlation

To see the table, make sure that your config.py file specifies show_correlations = True, then run pheweb serve. The demonstration data provided is intended to show correlations for the snowstorm phenotype: http://0.0.0.0:5000/pheno/snowstorm

TODO

abought commented 4 years ago

A version of this feature was since merged to master. I'm closing this PR as an artifact, but feel free to reopen if it's still relevant.