_pkgdown.yml

url: https://qile0317.github.io/APackOfTheClones/

development:
  mode: auto

template:
  bootstrap: 5
  includes:
    in_header: |
      <!-- Global site tag (gtag.js) - Google Analytics -->
      <script async src="https://www.googletagmanager.com/gtag/js?id=G-TSDH5XEN3S"></script>
      <script>
        window.dataLayer = window.dataLayer || [];
        function gtag(){dataLayer.push(arguments);}
        gtag('js', new Date());

        gtag('config', 'G-TSDH5XEN3S');
      </script>

redirects:
  - ["articles/web_only/Clonal_expansion_plotting.html", "articles/archive/v0-main.html"]

navbar:
  structure:
    left:  [install, intro, vignettes, reference, news, archive]
  components:
    install:
      text: Install
      href: articles/APackOfTheClones-install.html
    vignettes:
      text: Vignettes
      menu:
      - text: Storing and Fine-Tuning APackOfTheClones Runs
        href: articles/APackOfTheClones-runs.html
      - text: Working With Clonotypes Shared Across Clusters
        href: articles/APackOfTheClones-shared.html
      - text: Clonal Analysis Utilities in APackOfTheClones
        href: articles/APackOfTheClones-utils.html
    archive:
      text: Archive
      menu:
        - text: v0.1.x main vignette
          href: articles/archive/v0-main.html

reference:
- title: Core functions
- contents:
  - vizAPOTC
  - RunAPOTC
  - APOTCPlot
  - AdjustAPOTC
- title: Working with RunAPOTC runs
- contents:
  - getApotcDataIds
  - getLastApotcDataId
  - containsApotcRun
  - renameApotcRun
  - deleteApotcData
- title: Further Customization of Clonal Expansion Plots
- contents:
  - showCloneHighlight
  - overlayLegend
  - removeLegend
- title: Clonal Analysis Utilities
- contents:
  - countCloneSizes
  - mergeCloneSizes
  - getSharedClones
  - getReductionCentroids
- title: Data
- contents:
  - combined_pbmc