All stat and plot generation functions - #3
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Updated the Markdown design because the tables were coming out as weird piles of spaghetti instead. Added a helper function to simplify some of the repeated operations. Added new package to DESCRIPTION file. Plots have issues with labels clipping out of view, TBA.
metadata.parquet is generated from S. argenteus, and this parquet is being added for testing functions in this PR.
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The script works with the example
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AbhirupaGhosh
marked this pull request as ready for review
July 27, 2026 22:49
- add custom colors based on other 2 packages - cleanup and sort results from summarization fn - cleaned up titles/labels in both functions - generated example PDF, MD, HTML - rm oneoff dependencies like treemap + unused kableExtra - consistency check between 'resistant isolates' vs. 'AMR isolates' vs. genomes in some cases. still needs checking.
jananiravi
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Jul 27, 2026
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Looks good. Left a few comments for revision.
- Include total observations, unique genome IDs, and associated publications. - Detail antibiotics and antibiotic classes with counts. - Present phenotype counts and resistant proportions per antibiotic and class. - Summarize laboratory methods, collection years, isolation countries, sources, and hosts.
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I addressed @jananiravi 's comments and suggestions. |
jananiravi
previously approved these changes
Jul 28, 2026
…own file due to redundancy in documentation.
eboyer221
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Jul 28, 2026
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Thanks for the quick turnaround on the changes we discussed @AbhirupaGhosh! Confirming everything's resolved.
Holding off on tests for now, but we can follow up in a later PR. Approving.
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