_pkgdown.yml

url: https://prabhakarlab.github.io/Banksy

development:
  mode: auto
  
template:
  bootswatch: simplex

reference:
  - title: Neighborhood matrix computation
    contents:
      - computeBanksy
      - getBanksyMatrix
  - title: Dimensionality reduction
    contents:
      - runBanksyPCA
      - runBanksyUMAP
  - title: Clustering
    contents:
      - clusterBanksy
      - connectClusters
      - compareClusters
      - smoothLabels
      - clusterNames
  - title: Datasets
    contents: 
      - hippocampus
      - rings
  - title: Misc.
    contents:
      - simulateDataset

news:
  cran_dates: false

navbar:
  title: ~
  type: default
  left:
    - text: Functions and data
      href: reference/index.html
    - text: Vignettes
      menu:
      - text: BANKSY parameter selection (VeraFISH Mouse Hippocampus)
        href: articles/parameter-selection.html
      - text: Domain segmentation (STARmap PLUS Mouse brain)
        href: articles/domain-segment.html
      - text: Spatial data integration with Harmony (10x Visium Human DLPFC)
        href: articles/batch-correction.html
      - text: Analysing multiple datasets (10x Visium Human DLPFC)
        href: articles/multi-sample.html
    - text: News
      href: news/index.html