_pkgdown.yml

template:
  bootstrap: 3

url: https://github.com/KlugerLab/LocalizedMarkerDetector

reference:
  - title: "Construct Cell Graphs"
    # desc: >
    #   Construct cell graphs
    contents:
      - '`ConstructKnnGraph`'
      - '`ConstructDiffusionOperators`'
  - title: "Calculate LMD Score"
    # desc: >
    #   Calculate and visualize diffusion scores.
    contents:
      - '`LMD`'
      - '`fast_get_lmds`'
      - '`show_result_lmd`'
  - title: "Obtain Gene Modules"
    # desc: >
    #   Identify gene modules
    contents:
      - '`CalculateGeneDistance`'
      - '`ClusterGenes`'
  - title: "Calculate Cell Module Scores"
    # desc: >
    #   Define cell module score based on the identifies gene modules.
    contents:
      - '`AddModuleActivityScore`'
  - title: "Visualization"
    contents:
      - '`VisualizeGraph`'
      - '`CustomFeaturePlot`'
      - '`VisualizeDiffusion`'
      - '`CustomModulePlot`'
      - '`VisualizeScorePattern`'
      - '`VisualizeGeneHeatmap`'
      - '`VisualizeGeneTSNE`'
  - title: "Other"
    contents:
      - '`RowwiseNormalize`'

navbar:
  structure:
    left:
    - home
    # - intro
    - reference
    - articles
    # - tutorials
    right: github
  components:
    reference:
      text: Reference
      href: reference/index.html
    # intro:
    #   text: Get started
    #   href: vignettes/index.html
    articles:
      text: Articles
      menu:
      - text: Example on mouse bone marrow scRNA-seq
        href: articles/LMD_demo.html
      - text: Application to cross-sample comparison
        href: articles/LMD_cross_comparison_demo.html
  right:
  - icon: fa-github
    href: https://github.com/KlugerLab/LocalizedMarkerDetector