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All stat and plot generation functions #3

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Merged
AbhirupaGhosh merged 19 commits into from
Jul 28, 2026
Merged

All stat and plot generation functions #3

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cbbf942
All stat and plot generation functions
AbhirupaGhosh Jan 21, 2026
b0e7ead
Revised markdown code to fix weird formatting
epbrenner Jan 21, 2026
bf44340
Replace 'antibiotic' with 'drug_abbr' in plots
AbhirupaGhosh Jan 21, 2026
99f8066
Refactor genome_id references in amRdataPlots.R
AbhirupaGhosh Jun 4, 2026
630e0c8
Style code (GHA)
AbhirupaGhosh Jun 4, 2026
d9b39d1
Merge branch 'main' into generate_stat_plot
AbhirupaGhosh Jun 30, 2026
959e92e
Update amRdataPlots.R
AbhirupaGhosh Jun 30, 2026
48466d0
Update amRdataPlots.R
AbhirupaGhosh Jun 30, 2026
6e86396
Update amRdataPlots.R
AbhirupaGhosh Jul 1, 2026
1ec7b9f
Style code (GHA)
AbhirupaGhosh Jul 1, 2026
ae451e0
Adding some test data
epbrenner Jul 27, 2026
9a6e193
update summary/plot functions
jananiravi Jul 27, 2026
f7cd204
Add AMR summary report for Staphylococcus argenteus
AbhirupaGhosh Jul 28, 2026
3f26a76
Style code (GHA)
AbhirupaGhosh Jul 28, 2026
a5b4c76
Update plot titles for clarity in AMR data visualizations
AbhirupaGhosh Jul 28, 2026
3b41fcc
Merge branch 'generate_stat_plot' of https://github.com/JRaviLab/amRd…
AbhirupaGhosh Jul 28, 2026
c758dce
Fix laboratory typing method categorization in summary report
AbhirupaGhosh Jul 28, 2026
e6130f7
Add missing gridExtra/grid deps, regenerate NAMESPACE/man, fix indent…
eboyer221 Jul 28, 2026
1a28565
Update drug class phenotype count and Remove AMR summary report markd…
AbhirupaGhosh Jul 28, 2026
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5 changes: 4 additions & 1 deletion DESCRIPTION
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Expand Up @@ -34,7 +34,11 @@ Imports:
data.table,
dplyr,
duckdb,
ggplot2,
glue,
grid,
gridExtra,
knitr,
purrr,
readr,
reshape2,
Expand All @@ -44,7 +48,6 @@ Imports:
biocViews: GenomeAssembly, Annotation, Sequencing
VignetteBuilder: knitr
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
Config/roxygen2/version: 8.0.0
2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -6,6 +6,8 @@ export(CDHIT2duckdb)
export(buildClusterFeatureMap)
export(cleanData)
export(cleanMetaData)
export(generatePlots)
export(generateSummary)
export(prepareGenomes)
export(proteinAnnotations2Duckdb)
export(retrieveGenomes)
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