RGraphSpace/_pkgdown.yml at main · sysbiolab/RGraphSpace · GitHub

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url: https://sysbiolab.github.io/RGraphSpace/

destination: docs

template:
  bootstrap: 5
  bootswatch: flatly
  math-rendering: mathjax
  includes:
    in_header: |
      <style>
        .contents h1, .page-header h1 {
          font-size: 2.2rem !important;
          font-weight: 700 !important;
          margin-bottom: 1rem !important;
        }
        .contents h2 {
          font-size: 1.6rem !important;
          margin-top: 2rem !important;
        }
        body pre.sourceCode,
        body pre.sourceCode code.sourceCode {
          line-height: 1.5 !important;
        }
        span.co {
          font-size: 90% !important;
        }
      </style>

navbar:
  title: "RGraphSpace"
  left:
    - text: "Install"
      href: articles/install.html
    - text: "Get Started"
      href: articles/get-started.html
    - text: "Vignettes"
      menu:
      - text: "Introductory vignettes"
        header: true
      - text: "Building a graph space"
        href: articles/building-graphspace.html
      - text: "Customizing aesthetics"
        href: articles/customizing-aesthetics.html
      - text: "Fine-tuning scales and offsets"
        href: articles/scales-and-offsets.html
      - text: "Curved edges and loops"
        href: articles/curved-edges.html
      - text: "Geometries"
        href: articles/geometries.html
      - text: -------
      - text: "General applications"
        header: true
      - text: "Mapping graphs to images"
        href: articles/mapping-images.html
      - text: "Interoperability: ggraph & sf"
        href: articles/interoperability.html
      - text: "Interactive visualization"
        href: articles/interactive.html
      - text: -------
      - text: "Advanced workflows"
        header: true
      - text: "High-dimensional data"
        href: articles/high-dimensional.html
      - text: "Spatial feature data"
        href: articles/spatial-data.html
      - text: "Spatial segmentation with Seurat"
        href: articles/spatial-segmentation1.html
      - text: "Spatial segmentation with SpatialExperiment"
        href: articles/spatial-segmentation2.html
      - text: "Nested geometries and high-resolution images"
        href: articles/spatial-segmentation3.html
    - text: Index
      href: reference/index.html

reference:

- title: GraphSpace
  contents:
    - GraphSpace-class
    - GraphSpace
    - as.GraphSpace
    - getGraphSpace
    - updateGraphSpace
    - normalizeGraphSpace
    - cropGraphSpace
    - summary,GraphSpace-method

- title: Accessors
  contents:
    - GraphSpace-accessors

- title: Graph manipulation
  contents:
    - gs_subset
    - gs_add_nodes
    - gs_add_edges
    - GraphSpace-subscript

- title: Features
  contents:
    - gs_features-utils

- title: Geometry manipulation
  contents:
    - normalizeGeometry
    - fitGeometry

- title: ggplot2 integration
  contents:
    - ggplot-GraphSpace
    - inject_nodespace

- title: Geoms
  contents:
    - geom_nodespace
    - geom_edgespace
    - geom_graphspace

- title: Annotation
  contents:
    - annotation_gspace_image

- title: Plotting
  contents:
    - plotGraphSpace
    - plot.GraphSpace

- title: Themes
  contents:
    - theme_gspace

- title: Utilities
  contents:
    - as_colorraster
    - sfshape_stars
    - sfshape_ngons

- title: Data
  contents:
    - gtoys
    - gs_image_toy

- title: Internal
  contents:
    - GeomEdgeSpace
    - GeomNodeSpace
    - StatEdgeSpace
    - StatNodeSpace

- title: Package
  contents:
    - RGraphSpace-package

home:
  sidebar:
    structure: [links, license, community, citation, dev]
    components:
      dev:
        title: Developers
        text: |
          <ul class="list-unstyled">
            <li>Sysbiolab Team</li>
            <li><a href="authors.html">More about authors...</a></li>
          </ul>

footer:
  structure:
    left: developed_by
    right: built_with
  components:
    developed_by: "Developed by Sysbiolab"