_pkgdown.yml

url: https://somalogic.github.io/SomaPlotr

development:
  mode: auto

authors:
  Amanda Hiser:
    href: https://github.com/amanda-hi
  Stu Field:
    href: https://github.com/stufield
  SomaLogic Operating Co., Inc.:
    href: http://www.somalogic.com
  footer:
    roles: [fnd]
    text: "was developed by the Bioinformatics Dept. at"
  sidebar:
    roles: [cre, fnd]
    before: "Special :pray: to:"
    after: ":dna:"
  before: "[SomaPlotr](https://github.com/SomaLogic/SomaPlotr/) is proudly brought to you by:"
  after: ":dna:"

footer:
  structure:
    left: [logo, package, developed_by]
    right: built_with
  components:
    logo: "<img src='favicon-16x16.png'>"

template:
  bootstrap: 5
  package: tidytemplate
  bslib:
    #bg: "#202123"      # dark theme
    #fg: "#B8BCC2"      # dark theme
    primary: "#0054AD"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem
    base_font: {google: "Roboto"}

home:
  sidebar:
    structure: [links, help, oss, license, citation, authors, dev, toc]
    components:
      oss:
        title: Other Software
        text: >
          [SomaDataIO](https://somalogic.github.io/SomaDataIO/) <br />
          [SomaScan.db](https://somalogic.github.io/SomaScan.db/) <br />
          [Canopy (Python)](https://github.com/SomaLogic/Canopy/) <br />
          [DataDelve Statistics](https://somalogic.com/datadelve-statistics/)
      help:
        title: Getting Help
        text: >
          [Ask a question](https://somalogic.github.io/SomaPlotr/SUPPORT.html) <br />
          [Report a bug](https://github.com/SomaLogic/SomaPlotr/issues)
  links:
  - text: Learn more about SomaScan
    href: http://www.somalogic.com
  - text: Read SomaScan tech notes
    href: http://www.somalogic.com/tech-notes/

navbar:
  structure:
    left: [intro, reference, articles, soon, news]
    right: [search, github]
  components:
    soon:
      text: Coming Soon
      menu:
      - text: Plotting SomaScan
      - text: ---
      - text: Distributions (PDF/CDF)
      - text: Plot Scale Factors
      - text: ROC Curves

articles:
  - title: Getting Started
    navbar: ~
    contents:
    - SomaPlotr

  - title: Applying SomaLogic Themes and Palettes
    navbar: ~
    contents:
    - themes-and-palettes

reference:
  - title: SomaLogic `ggplot2`-style
    desc: >
      Use themes, palettes, and scales to generate `ggplots` with
      consistent style and format.
    contents:
    - ends_with("_soma")
    - starts_with("style-")

  - title: Concordance
    desc: >
      Plotting concordance of two continuous variables.
    contents:
    - plotConcord

  - title: CDFs and PDFs
    desc: >
      Plotting cumulative distribution functions (CDF)
      and probability density functions (PDF).
    contents:
    - contains("CDF")
    - contains("PDF")
    - addCDFquantiles

  - title: Volcano Plots
    desc: >
      Plotting volcanos.
    contents:
    - starts_with("plotVolcano")

  - title: Longitudinal data
    desc: >
      Plotting time series or longitudinal traces.
    contents:
    - plotLongitudinal
    - plotPolygon

  - title: Boxplot graphics
    desc: >
      Various forms of boxplots.
    contents:
    - starts_with("boxplot[A-Z]")

  - title: Maps
    desc: >
      Plotting maps; "fold-change", "outlier", and "missingness".
    contents:
    - starts_with("calc[A-Z]")
    - plot.Map
    - getFlaggedIds

  - title: Histograms
    desc: >
      Various forms of histograms.
    contents:
    - ends_with("Hist")

  - title: Exporting base plots
    desc: >
      Useful utilities to save plots to file.
    contents:
    - figure

  - title: Package Data
    desc: >
      Data objects in `SomaPlotr`.
    contents:
    - objects

news:
  - one_page: true