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All stat and plot generation functions - #3

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AbhirupaGhosh merged 19 commits into
mainfrom
generate_stat_plot
Jul 28, 2026
Merged

All stat and plot generation functions#3
AbhirupaGhosh merged 19 commits into
mainfrom
generate_stat_plot

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@AbhirupaGhosh

@AbhirupaGhoshAbhirupaGhosh commented Jan 21, 2026

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Description

What kind of change(s) are included?

  • Feature (adds or updates new capabilities)
  • Bug fix (fixes an issue).
  • Enhancement (adds functionality).
  • Breaking change (these changes would cause existing functionality to not work as expected).

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Please ensure that all boxes are checked before indicating that this pull request is ready for review.

  • I have read and followed the CONTRIBUTING.md guidelines.
  • I have searched for existing content to ensure this is not a duplicate.
  • I have performed a self-review of these additions (including spelling, grammar, and related).
  • I have added comments to my code to help provide understanding.
  • I have added a test which covers the code changes found within this PR.
  • I have deleted all non-relevant text in this pull request template.
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@AbhirupaGhoshAbhirupaGhosh self-assigned this Jan 21, 2026
epbrennerand others added 3 commits January 20, 2026 17:42
@epbrenner
Revised markdown code to fix weird formatting
b0e7ead
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.
@AbhirupaGhosh
Replace 'antibiotic' with 'drug_abbr' in plots
bf44340
@AbhirupaGhosh
Refactor genome_id references in amRdataPlots.R
99f8066
@AbhirupaGhosh

AbhirupaGhosh commented Jul 27, 2026

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The script works with the example metadata.parquet with the following calls.

source("R/amRdataPlots.R")
generateSummary("data/metadata.parquet", out_path = "data/")
generatePlots("data/metadata.parquet", out_path = "data/")

@AbhirupaGhosh
AbhirupaGhosh marked this pull request as ready for review July 27, 2026 22:49
@jananiravi
update summary/plot functions
9a6e193
- 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
jananiravi requested changes Jul 27, 2026
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@jananiravijananiravi left a comment

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Looks good. Left a few comments for revision.

Comment threadR/utils_colors.R
Comment threadR/amRdataPlots.R
Comment threadR/amRdataPlots.R
Comment threadR/amRdataPlots.R Outdated
Comment threadR/amRdataPlots.R Outdated
Comment threadR/amRdataPlots.R
AbhirupaGhoshand others added 4 commits July 27, 2026 18:12
@AbhirupaGhosh
Add AMR summary report for Staphylococcus argenteus
f7cd204
- 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.
@AbhirupaGhosh
Style code (GHA)
3f26a76
@AbhirupaGhosh
Update plot titles for clarity in AMR data visualizations
a5b4c76
@AbhirupaGhosh
Merge branch 'generate_stat_plot' ofhttps://github.com/JRaviLab/amRdata
3b41fcc
 into generate_stat_plot
@AbhirupaGhosh

AbhirupaGhosh commented Jul 28, 2026

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I addressed @jananiravi 's comments and suggestions.

jananiravi
jananiravi previously approved these changes Jul 28, 2026
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Comment threaddata/amr_metadata_summary.md Outdated
eboyer221
eboyer221 approved these changes 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.

@AbhirupaGhosh
AbhirupaGhosh merged commit b43ba33 into mainJul 28, 2026
@AbhirupaGhosh
AbhirupaGhosh deleted the generate_stat_plot branch July 28, 2026 16:58
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@eboyer221eboyer221eboyer221 approved these changes
@jananiravijananiravijananiravi left review comments
@epbrennerepbrennerAwaiting requested review from epbrenner
@charmvangcharmvangAwaiting requested review from charmvang

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