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Add inferred sex tables to stats page

Open rileyhgrant opened this issue 1 year ago • 2 comments

Resolves #1355

Adds 2 tables to the stats page that display the number of inferred sex sample per genetic ancestry group in v4

rileyhgrant avatar Feb 09 '24 18:02 rileyhgrant

Screenshots of tables:

Screenshot 2024-02-12 at 13 46 38

Screenshot 2024-02-12 at 13 46 45

Location of tables on page:

Screenshot 2024-02-12 at 13 45 03

rileyhgrant avatar Feb 12 '24 19:02 rileyhgrant

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.

ch-kr avatar Feb 12 '24 20:02 ch-kr

Related: https://github.com/broadinstitute/gnomad_production/issues/1589

rileyhgrant avatar May 02 '24 00:05 rileyhgrant

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."

rileyhgrant avatar May 23 '24 20:05 rileyhgrant

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

  1. Updated diversity table

    Screenshot 2024-06-17 at 15 11 02

  2. V4 XX/XY

    Screenshot 2024-06-17 at 15 11 17

  3. V4 Non-UKB XX/XY Screenshot 2024-06-17 at 15 11 28

  4. Location of new tables on stats page

    Screenshot 2024-06-17 at 15 12 03

rileyhgrant avatar Jun 17 '24 20:06 rileyhgrant