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Fix "square": True for scatter plot. Make the GATK BaseRecalibrator plot square #2189

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merged 7 commits into from Nov 21, 2023
Merged

Fix "square": True for scatter plot. Make the GATK BaseRecalibrator plot square #2189

merged 7 commits into from Nov 21, 2023

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vladsavelyev
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@vladsavelyev vladsavelyev commented Nov 17, 2023 •
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Fix #2182

  • Pass "square" to the plot config
  • Set xmin=0 and ymax=0 .
  • Assure xmax == xmin in the python plotting code.
  • Fix the scatter plot plotting code to re-calculate the total max value, pass endOfTick and calculate padding manually to make sure HighCharts doesn't get creative with padding

@vladsavelyev vladsavelyev added the awaits-review Awaiting final review and merge. label Nov 20, 2023
@vladsavelyev vladsavelyev changed the title GATK: make base recalibrator plot square GATK: make BaseRecalibrator plot square. Fix the "square" scatter plot option Nov 20, 2023
@vladsavelyev vladsavelyev changed the title GATK: make BaseRecalibrator plot square. Fix the "square" scatter plot option Fix "square": True for scatter plot. Make the GATK BaseRecalibrator plot square Nov 20, 2023
@vladsavelyev vladsavelyev added this to the MultiQC v1.19 milestone Nov 20, 2023
@vladsavelyev vladsavelyev mentioned this pull request Nov 20, 2023
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ewels
ewels approved these changes Nov 21, 2023
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LGTM 👍🏻

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ewels commented Nov 21, 2023

Nice, thanks! Did you get the diagonal extra_series line to work in the end?

That's minor though, not worth holding up the PR for.

@ewels ewels merged commit fa2e848 into master Nov 21, 2023
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@ewels ewels deleted the sqaure-gatk-base-recal branch November 21, 2023 10:08
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awaits-review Awaiting final review and merge. core: front end module: enhancement
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GATK: Rescale Emperical Quality scatter plot
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