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fix: relative aggregation sample plot #412

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merged 12 commits into from
Jan 4, 2022

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AKBrueggemann
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Description

Changed the threshold values for the lineages and variants over time plots. The threshold for the plotting of a lineage or variant is now depending on the number of lineages/variants available for the given number of samples.

Related Issue

#339

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@thomasbtf
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I think if we do it with the if statements, we have to visit this every now and then again, because of the hardcoded length check.

Maybe we can select the x top lineages by doing the following:

  1. Get the total occurrence per lineage (e.g. by filtering down the pangolin_calls["lineage_count"] column on the unique entries per lineage). link
  2. Sort it. link.
  3. Get the top 10 or 20 lineages. Maybe we can use this.
  4. Mask every lineage that is not in that selected group.

@thomasbtf
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This still has to be changed, bis don't merge

@thomasbtf thomasbtf marked this pull request as draft December 23, 2021 15:23
@thomasbtf thomasbtf marked this pull request as ready for review January 4, 2022 07:42
@thomasbtf thomasbtf merged commit 6a8155e into master Jan 4, 2022
@thomasbtf thomasbtf deleted the relative-aggregation-sample-plot branch January 4, 2022 07:43
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3 participants