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Add inferred sex tables to stats page #1416

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Resolves #1355

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

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@phildarnowsky-broad phildarnowsky-broad left a comment

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One tiny cleanup and a general comment, good to go otherwise.

@rileyhgrant
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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

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ch-kr commented Feb 12, 2024

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.

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@rileyhgrant rileyhgrant force-pushed the add-stats-page-inferred-sex-tables branch from 5f5de61 to f431932 Compare May 23, 2024 18:22
@rileyhgrant rileyhgrant force-pushed the add-stats-page-inferred-sex-tables branch from eaa1fa4 to e611668 Compare May 23, 2024 19:56
@rileyhgrant
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rileyhgrant commented May 23, 2024

Commenting checklist for myself:

  • Use iteration to render tables
  • Add XX and XY to diversity table for v4
  • Re-order ancestry groups to be consistent with table higher up on page
  • "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)
  • remove empty columns from non-ukb 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."

@rileyhgrant rileyhgrant force-pushed the add-stats-page-inferred-sex-tables branch from a427c7d to 35b397e Compare May 24, 2024 17:54
@rileyhgrant rileyhgrant force-pushed the add-stats-page-inferred-sex-tables branch from 0835d91 to 1e9d7cd Compare May 24, 2024 18:12
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Add counts of inferred sex per genetic ancestry group
3 participants