_quarto.yml

project:
  type: book
  output-dir: docs

execute:
  freeze: auto

book:
  title: "Spatial analysis playbook"
  author: "Alex Qin, Shreya Rao, Farhan Ameen, Ellis Patrick"
  date: "`r Sys.Date()`"
  chapters:
    - part: "Overview"
      contents:
        - index.qmd
        - packages.qmd
        - datasets.qmd
        - getting_started.qmd
    - part: "Processing"
      contents:
        - 01-processing.qmd
        - 02-quality_control.qmd
    - part: "Cell annotation"
      contents:
        - 03a-cell_annotation.qmd
        - 03b-cell_annotation.qmd
    - part: "Cell localisation"
      contents:
        - 04a-cell_localisation.qmd
        - 04b-cell_localisation_parent.qmd
    - part: "Spatial domains"
      contents:
        - 05-cellular_niches.qmd
    - part: "Marker expression"
      contents:
        - 06-changes_in_marker_expression.qmd
    - part: "Classification"
      contents:
        - 07-classification.qmd
    - part: "Case studies"
      contents:
        - 08-case_study1.qmd
    - part: "References"
      contents:
        - 09-references.qmd
  navbar:
    logo: images/USydLogo.svg

bibliography: references.bib

format:
  html:
    theme: [cosmo, styles.scss]
    css: styles.css
    toc: true
    code-link: true

editor: visual