_pkgdown.yml

url: https://bailey-lab.github.io/miplicorn/

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    base_font: { google: "Lato" } # usually serif fonts
    heading_font: { google: "Fira Sans" } # usually sans-serif fonts
    code_font: { google: "Fira Code" } # usually monospace fonts
    pkgdown-nav-height: 75px

navbar:
  structure:
    left: [intro, reference, articles, news]
    right: [search, github]
  components:
    news:
      text: News
      menu:
        - text: "Change log"
          href: news/index.html

development:
  mode: auto

authors:
  Aris Paschalidis:
    href: "https://www.arispas.com/"

reference:
  - title: Parse
    desc: >
      These functions parse files obtained from
      [MIPTools](https://github.com/bailey-lab/MIPTools) into tibbles.
    contents:
      - read-tbl
      - label_mutations

  - title: Manipulate
    desc: >
      These functions are used to manipulate data objects.
    contents:
      - filter
      - mutation_prevalence
      - mutation_frequency
      - convert_single
      - arrange_natural

  - title: Visualize
    desc: >
      These functions are used to visualize data.
    contents:
      - chromosome-map
      - plot_coverage
      - plot_mutation_prevalence
      - plot_mutation_frequency
      - theme_miplicorn

  - title: Miscellaneous
    desc: >
      These functions are used to inspect objects.
    contents:
      - miplicorn_example

  - title: Data
    contents:
      - genome_Pf3D7

articles:
  - title: Using miplicorn
    desc:
    navbar: ~
    contents:
      - miplicorn
      - large-files
      - faq