Implement as package

.Rbuildignore

@@ -0,0 +1,13 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE$
+^environment\.yml$
+^QC_report\.ipynb$
+^QC_report_files$
+^\.quarto$
+^\.cursor$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^data-raw$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,134 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Pushes to main deploy the site to the root of GitHub Pages. Pull requests
+# from this repository deploy a preview to preview/pr-<number>/, which is
+# removed when the pull request is closed.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    types: [opened, synchronize, reopened, closed]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+env:
+  SITE_URL: https://eppicenter.github.io/ampseq-qc/
+
+jobs:
+  pkgdown:
+    if: github.event.action != 'closed'
+    runs-on: ubuntu-latest
+    concurrency:
+      group: pkgdown-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      PREVIEW_DIR: ${{ github.event_name == 'pull_request' && format('preview/pr-{0}', github.event.pull_request.number) || '' }}
+      CAN_DEPLOY: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository }}
+    permissions:
+      contents: write
+      pull-requests: write
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Build site
+        run: |
+          preview_dir <- Sys.getenv("PREVIEW_DIR")
+          override <- if (nzchar(preview_dir)) list(url = paste0(Sys.getenv("SITE_URL"), preview_dir)) else list()
+          pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, override = override)
+        shell: Rscript {0}
+
+      - name: Render example QC report
+        run: |
+          tutorial <- system.file("extdata", "tutorial", package = "ampseqQC")
+          ampseqQC::render_qc_report(
+            results_dir = file.path(tutorial, "results"),
+            manifest_file = file.path(tutorial, "manifest.csv"),
+            output_dir = "docs/example-report"
+          )
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: true
+          clean-exclude: preview
+          branch: gh-pages
+          folder: docs
+
+      # Keeps GitHub Pages from running Jekyll before the main site has been deployed
+      - name: Add .nojekyll to GitHub pages root
+        if: github.event_name == 'pull_request' && env.CAN_DEPLOY == 'true'
+        run: mkdir -p pages-root && touch pages-root/.nojekyll
+
+      - name: Deploy .nojekyll to GitHub pages
+        if: github.event_name == 'pull_request' && env.CAN_DEPLOY == 'true'
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: pages-root
+
+      - name: Deploy preview to GitHub pages
+        if: github.event_name == 'pull_request' && env.CAN_DEPLOY == 'true'
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: true
+          branch: gh-pages
+          folder: docs
+          target-folder: ${{ env.PREVIEW_DIR }}
+
+      - name: Comment preview link
+        if: github.event_name == 'pull_request' && env.CAN_DEPLOY == 'true'
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: pkgdown-preview
+          message: |
+            📖 Documentation preview for ${{ github.event.pull_request.head.sha }}:
+
+            * Site: ${{ env.SITE_URL }}${{ env.PREVIEW_DIR }}/
+            * Tutorial: ${{ env.SITE_URL }}${{ env.PREVIEW_DIR }}/articles/ampseqQC.html
+            * Example report: ${{ env.SITE_URL }}${{ env.PREVIEW_DIR }}/example-report/QC_report.html
+
+            GitHub Pages can take a minute or two to update.
+
+  remove-preview:
+    if: github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.head.repo.full_name == github.repository
+    runs-on: ubuntu-latest
+    concurrency:
+      group: pkgdown-${{ github.event.pull_request.number }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: gh-pages
+
+      - name: Remove preview
+        run: |
+          preview_dir="preview/pr-${{ github.event.pull_request.number }}"
+          if [ -d "$preview_dir" ]; then
+            git config user.name "github-actions[bot]"
+            git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git rm -r --quiet "$preview_dir"
+            git commit -m "Remove documentation preview for PR #${{ github.event.pull_request.number }}"
+            git push
+          fi

.gitignore

@@ -42,6 +42,9 @@ vignettes/*.pdf
 # pkgdown site
 docs/
 
+# built vignettes
+inst/doc
+
 # translation temp files
 po/*~
 

DESCRIPTION

@@ -1,9 +1,39 @@
-Package: ampseq-qc
+Package: ampseqQC
 Type: Package
-Title: QC Summary Shiny App
+Title: Quality Control Reports for Mad4hatter Amplicon Sequencing Runs
 Version: 0.1.0
-Author: EPPIcenter
-Maintainer: kathryn.murie@ucsf.edu
-Description: A Shiny app for visualizing QC summary data from ampseq data
-Depends: R (>= 3.5.0), shiny, shinyFiles, ggplot2, dplyr, tidyr, ggbeeswarm, stringr
-License: MIT
+Authors@R: c(
+    person("Kathryn", "Murie", email = "kathryn.murie@ucsf.edu", role = c("aut", "cre")),
+    person("EPPIcenter", role = "cph")
+    )
+Description: Summarises quality control statistics for targeted amplicon
+    sequencing runs processed with the Mad4hatter pipeline, combining pipeline
+    outputs with a sample manifest. Provides functions to load results, assign
+    targets to multiplex PCR reactions from their pools, classify samples as
+    pass, repool or reprep, summarise positive and negative controls, filter
+    allele tables, and render an HTML QC report.
+License: GPL-3
+URL: https://eppicenter.github.io/ampseq-qc/, https://github.com/EPPIcenter/ampseq-qc
+BugReports: https://github.com/EPPIcenter/ampseq-qc/issues
+Encoding: UTF-8
+Depends:
+    R (>= 4.1.0)
+Imports:
+    dplyr (>= 1.1.0),
+    ggbeeswarm,
+    ggplot2,
+    kableExtra,
+    knitr,
+    plotly,
+    purrr,
+    rlang,
+    tibble,
+    tidyr
+Suggests:
+    rmarkdown,
+    testthat (>= 3.0.0),
+    withr
+VignetteBuilder: knitr
+Config/testthat/edition: 3
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3

NAMESPACE

@@ -0,0 +1,58 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(print,ampseqQC_panel_settings)
+export(add_allele_frequency)
+export(allele_table_group_cols)
+export(assign_reactions)
+export(check_sample_names)
+export(count_targets_per_reaction)
+export(create_plate_template)
+export(create_tabset)
+export(default_panel_settings)
+export(fill_missing_data)
+export(filter_allele_table)
+export(generate_balancing_plot)
+export(generate_dimer_plot)
+export(generate_parasitemia_by_amplification_success_plot)
+export(generate_parasitemia_by_amplification_success_plots)
+export(generate_reads_by_amplification_success_plot)
+export(generate_reads_by_amplification_success_plots)
+export(generate_reprep_repool_table)
+export(interactive_plot)
+export(merge_amplicon_coverage)
+export(merge_sample_coverage)
+export(missing_samples_report)
+export(missing_targets_report)
+export(negative_control_amplicons)
+export(negative_control_plot_height)
+export(negative_control_targets_over_threshold)
+export(panel_settings)
+export(plot_negative_control_histogram)
+export(plot_negative_control_target_reads)
+export(plot_plate)
+export(plot_plate_heat_maps)
+export(plot_plate_layouts)
+export(plot_plate_with_feature)
+export(plot_positive_control_alleles)
+export(plot_qc_status_by_batch)
+export(print_sized_plot)
+export(qc_excluded_targets)
+export(qc_report_template)
+export(qc_status_counts)
+export(qc_summary_by_batch)
+export(qc_summary_table)
+export(read_mad4hatter_results)
+export(read_manifest)
+export(render_qc_report)
+export(sample_counts_by_file)
+export(sample_name_mismatches)
+export(sample_qc_status)
+export(samples_missing_from_allele_data)
+export(samples_with_status)
+export(standardise_illumina_sample_name)
+export(styled_table)
+export(summarise_negative_control_targets)
+export(summarise_pools)
+export(summarise_positive_controls)
+export(summarise_samples)
+importFrom(dplyr,"%>%")