_pkgdown.yml

url: http://akoyabio.github.io/phenoptr

template:
  params:
    bootswatch: cerulean

navbar:
  type: inverse
  title: "phenoptr"
  left:
    - icon: fa-home fa-lg
      href: index.html
    - text: "Tutorials"
      menu:
        - text: "Reading and exploring inForm tables"
          href: articles/reading_tables.html
        - text: "Computing inter-cellular distances"
          href: articles/computing_distances.html
        - text: "Find and count touching cells"
          href: articles/find_and_count_touching_cells.html
        - text: "Reading and displaying inForm image Files"
          href: articles/reading_image_files.html
        - text: "Selecting cells within a cell segmentation table"
          href: articles/selecting_cells.html
    - text: "Reference"
      href: reference/index.html
  right:
   - icon: fa-newspaper-o
     text: "news"
     href: news/index.html
   - icon: fa-github fa-lg
     text: github
     href: https://github.com/akoyabio/phenoptr

articles:
  - title: Tutorials
    contents:
    - reading_tables
    - computing_distances
    - find_and_count_touching_cells
    - reading_image_files
    - selecting_cells

reference:
  - title: "Package options"
    contents:
      - phenoptr-package
  - title: "Read and preprocess inForm data and image files"
    contents:
      - list_cell_seg_files
      - read_cell_seg_data
      - get_field_info
      - get_map_path
      - read_components
      - read_composite_info
      - read_composites
      - read_field_info
      - read_maps
      - parse_tissue_description
  - title: "Compute and visualize spatial relationships between cells"
    contents:
      - find_nearest_distance
      - compute_all_nearest_distance
      - count_within
      - count_within_batch
      - count_within_detail
      - count_within_many
      - count_touching_cells
      - count_touching_cells_fast
      - make_ppp
      - spatial_distribution_report
  - title: "Estimate cell density"
    contents:
      - density_bands
      - density_at_distance
  - title: "Helpers"
    contents:
      - distance_matrix
      - field_column
      - parse_phenotypes
      - phenotype_columns
      - plot_diverging
      - readTIFFDirectory
      - select_rows
      - subset_distance_matrix
      - unique_phenotypes
      - validate_phenotype_definitions
      - validate_phenotypes
  - title: "Sample data"
    contents:
      - sample_cell_seg_data