_pkgdown.yml

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

template:
  params:
    bootswatch: cerulean

navbar:
  type: inverse
  title: "phenoptrReports"
  left:
    - icon: fa-home fa-lg
      href: index.html
    - text: "Tutorials"
      menu:
        - text: "Consolidating inForm data"
          href: articles/consolidation.html
        - text: "Analyzing inForm data"
          href: articles/analysis.html
        - text: "Visualizing spatial relationships"
          href: articles/spatial_map_viewer.html
        - text: "Unmixing quality report"
          href: articles/unmixing_quality_report.html
        - text: "Mean of top 20 / bottom 10 cells report"
          href: articles/top_20_bottom_10_report.html
        - text: "Staining consistency report"
          href: articles/staining_consistency_report.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/phenoptrReports

articles:
  - title: Tutorials
    contents:
    - consolidation
    - analysis
    - spatial_map_viewer
    - unmixing_quality_report
    - component_levels_report
    - top_20_bottom_10_report
    - staining_consistency_report

reference:
  - title: RStudio Addins
    desc: These functions are added to the RStudio Addins menu. Selecting
          one opens a GUI.
    contents:
      - addin_10_merge
      - addin_20_consolidate
      - addin_30_analysis_app
      - addin_35_spatial_map_viewer
      - addin_40_unmixing_quality
      - addin_50_component_levels
      - addin_60_mean_of_top_and_bottom_cells
      - addin_70_staining_consistency_report
  - title: Merging and Consolidation
    desc: These functions implement the merge and consolidation apps.
    contents:
      - merge_cell_seg_files
      - consolidate_and_summarize_cell_seg_data
  - title: Calculations
    desc: These functions perform the calculations for an analysis.
    contents:
      - compute_density_from_cell_summary
      - compute_density_from_table
      - compute_h_score
      - compute_h_score_from_score_data
      - compute_mean_expression
      - compute_mean_expression_many
      - compute_positivity
      - compute_positivity_many
      - counts_to_percents
      - count_phenotypes
      - count_within_summary
      - nearest_neighbor_summary
  - title: Mean of top and bottom cells
    desc: These functions implement the Mean of top 20 / bottom 10 cells report
    contents:
      - mean_of_top_and_bottom_cells_report
      - mean_of_top_and_bottom_cells
      - write_mean_of_top_and_bottom_charts
  - title: Data reporting - HTML
    desc: These functions write analysis results to HTML reports.
    contents:
      - component_levels_report
      - staining_consistency_report
      - unmixing_quality_report
      - write_summary_report
  - title: Data reporting - Excel and Word
    desc: These functions write analysis results to Excel worksheets
          and Word documents.
    contents:
      - write_counts_sheet
      - write_count_within_sheet
      - write_density_sheet
      - write_expression_sheet
      - write_h_score_sheet
      - write_nearest_neighbor_summary_sheet
      - write_percents_sheet
      - write_plot_sheet
      - write_sheet
      - write_summary_charts
      - write_summary_sheet
  - title: Helper functions
    contents:
      - choose_directory
      - choose_files
      - discrete_colors
      - nearest_neighbor_map
      - order_by_slide_and_tissue_category
      - spatial_map_viewer
      - split_phenotypes
      - unmixing_quality_report
      - upset_plot
      - write_session_info

toc:
  depth: 4