fix: relative aggregation of samples for variants and lineages over time plots #382
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thomasbtf
suggested changes
Dec 8, 2021
| pangolin_calls["lineage_count"] < 10, "lineage" | ||
| ] = "other (< 10 occ.)" | ||
| pangolin_calls["lineage_count"] < threshold, "lineage" | ||
| ] = "other (< low occ.)" |
There was a problem hiding this comment.
Please insert here the masking threshold number. It would make sense to cast it to an integer before.
| threshold = len(calls) / 10 | ||
| calls.loc[ | ||
| calls["total occurrence"] < threshold, "alteration" | ||
| ] = "other (< low occ.)" |
|
Ah and please fill out the Description, Related Issue and Checklist of this PR ;) |
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Lineages over time of 5 samples: |
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Variants over time of the S-ORF of one sample: |
thomasbtf
approved these changes
Dec 9, 2021
|
Just a quick pointer to string formatting best practices: https://realpython.com/python-string-formatting/ :) |
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Description
Changing the threshold for the appearance of lineages and variants in the plots from a static to a relative value, so that for a smaller number of samples the variants and lineages are plotted.Related Issue
#339Checklist
snakefmt workflow/andblack workflow/if needed.CODE_OF_CONDUCT.mddocument.CONTRIBUTING.mdguide.