_pkgdown.yml

url: https://FertigLab.github.io/dominoSignal

deploy:
  install_metadata: true

template:
  bootstrap: 5
  theme: a11y-light
  bootswatch: zephyr
  bslib:
    primary: "#7DDED2"
    secondary: "#1D132B"
    pkgdown-nav-height: 100px
    nav-link-color: "#1D132B"
    nav-tabs-link-active-bg: "#DFD4EC"
    headings-color: "#457E78"
    component-active-bg: "#DFD4EC"
    code-font-size: 95%
    code-bg: "#FEFEFE"
    link-color: "#8963BA"
    border-color: "#F4F0FA"
    code_font: { google: "Fira Code" }
    border-width: 2px


reference:
- title: "Domino Classes"
  desc: >
    An object class designed to store information used 
    and produced in dominoSignal analysis
  contents:
  - domino-class
  - linkage_summary
- title: "Analysis Functions"
  desc: >
    Functions for performing cell-cell communication analysis
    with the dominoSignal package
  contents:
  - create_rl_map_cellphonedb
  - create_regulon_list_scenic
  - create_domino
  - build_domino
  - summarize_linkages
  - test_differential_linkages
- title: "Plotting Functions"
  desc: "Functions for visualizing dominoSignal analysis results"
- subtitle: "Heatmaps"
  contents:
  - cor_heatmap
  - feat_heatmap
  - incoming_signaling_heatmap
  - signaling_heatmap
- subtitle: "Network Plots"
  contents:
  - gene_network
  - signaling_network
- subtitle: "Other Plots"
  contents:
  - circos_ligand_receptor
  - cor_scatter
  - plot_differential_linkages
- title: "Helper Functions"
  desc: "Convenience functions for working with dominoSignal objects"
- subtitle: "Access functions"
  contents:
  - dom_clusters
  - dom_correlations
  - dom_counts
  - dom_database
  - dom_de
  - dom_info
  - dom_linkages
  - dom_network_items
  - dom_signaling
  - dom_tf_activation
  - dom_zscores
- subtitle: "Misc. utility functions"
  contents:
  - add_rl_column
  - count_linkage
  - mean_ligand_expression
  - print,domino-method
  - rename_clusters
  - show,domino-method
- title: "Example Data"
  desc: >
    Example data used for testing and demonstration purposes
  contents:
  - CellPhoneDB
  - SCENIC
  - PBMC
  - mock_linkage_summary

navbar:
  type: light
  structure:
    left:  [intro, articles, reference, news]
    right: [search, github]
    components:
      articles:
        text: Tutorials
        menu:
        - text: SCENIC for TF Scoring
          href: vignettes/articles/tf_scenic_vignette.html
        - text: Using CellphoneDB
          href: vignettes/articles/cellphonedb_vignette.html
        - text: Domino Object Structure
          href: vignettes/domino_object_vignette.html
        - text: Plotting and Visualization
          href: vignettes/plotting_vignette.html

home:
  title: Cell Communication from Single Cell RNA Sequencing Data
  description: >
    dominoSignal uses transcription factor activation and ligand - receptor linkages to infer intra- and inter- cellular signaling from single cell RNA sequencing data.
  sidebar:
    structure: [toc, authors, labs, citation, license]
    components:
      labs:
        title: Contributing Labs
        text: |
              For more information about these labs, click below.\n

              <a href=https://elisseefflab.jhu.edu/> Elisseeff Lab </a> \n

              <a href=https://fertiglab.com/> Fertig Lab </a>

footer:
  structure:
    left: [package, developed_by]
    right: built_with

news:
  one_page: true
  cran_dates: false
  releases:
  - text: "dominoSignal v0.2.1"
    href: https://github.com/FertigLab/dominoSignal/releases/tag/v0.2.1-alpha
  - text: "dominoSignal v0.2.2"
    href: https://github.com/FertigLab/dominoSignal/releases/tag/v0.2.2-alpha
  - text: "dominoSignal v0.99.2"
    href: https://github.com/FertigLab/dominoSignal/releases/tag/v0.99.2-alpha
  - text: "dominoSignal v1.0.0 for Bioconductor"
    href: https://github.com/FertigLab/dominoSignal/releases/tag/v1.0.0-Bioconductor

authors:
  footer:
    roles: aut
    text: "is developed by"
  sidebar:
    roles: [aut, ctb]