gnomad-browser
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Add inferred sex tables to stats page
Resolves #1355
Adds 2 tables to the stats page that display the number of inferred sex sample per genetic ancestry group in v4
Screenshots of tables:
Location of tables on page:
thank you so much for working on this!
I have a few comments:
- I wonder if the counts per sex karyotype in the first new table (counts across all of v4) should get merged with the existing table? By this, I mean, it might be a good idea to add the Sample count, XX, and XY subheaders to the existing diversity table, and then merge AMI counts into Remaining / Finnish into European.
- Could you reorder the genetic ancestry groups in these new tables so that they match the same order in the diversity table?
- With the above, could you update the labels in the new tables so that they are the same as the ones in the currently displayed table (e.g., "African/African American" -> "African")
- I'd prefer not keeping the v4 Genomes / Combined columns in the new non-UKB sex table
One additional comment: since this update impacts the stats page, I think it'd be a good idea to post screenshots in #gnomad_browser to get feedback.
Related: https://github.com/broadinstitute/gnomad_production/issues/1589
Commenting checklist for myself:
- [x] Use iteration to render tables
- [x] Add XX and XY to diversity table for v4
- [x] Re-order ancestry groups to be consistent with table higher up on page
- [x] "With the above, could you update the labels in the new tables so that they are the same as the ones in the currently displayed table (e.g., "African/African American" -> "African")"
- I feel like going the opposite direction would be more consistent across the entire browser (make "African" -> "African/African American" in the currently displayed table)
- [x] remove empty columns from non-ukb table
- [x] "One additional comment: since this update impacts the stats page, I think it'd be a good idea to post screenshots in #gnomad_browser to get feedback."
Apologies for letting this hang out so long, going to post about this and merge soon since we have been getting somewhat regular requests for this.
New screenshots
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Updated diversity table
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V4 XX/XY
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V4 Non-UKB XX/XY
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Location of new tables on stats page