_pkgdown.yml

url: https://digitalcytometry.github.io/spatialecotyper

development:
  mode: auto

repo:
  url:
    home: https://github.com/digitalcytometry/spatialecotyper
    source: https://github.com/digitalcytometry/spatialecotyper
    issue: https://github.com/digitalcytometry/spatialecotyper/issues
  branch: main

template:
  bootswatch: simplex
  bootstrap: 5
  bslib:
    primary: "#0054AD"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem

authors:
  Wubing Zhang:
    href: https://profiles.stanford.edu/wubing-zhang
  Aaron Newman Lab:
    href: https://anlab.stanford.edu/

navbar:
  title: ~
  type: default
  left:
    - text: Vignettes
      menu:
      - text: Discovery of Spatial Ecotypes from a Single Sample
        href: articles/SingleSample.html
      - text: Discovery of Spatial Ecotypes from Multiple Samples
        href: articles/Integration.html
      - text: Development of NMF Models for Spatial Ecotype Recovery
        href: articles/TrainRecoveryModels.html
      - text: Recovery of Spatial Ecotypes from Spatial Transcriptomics Data
        href: articles/Recovery_Spatial.html
      - text: Recovery of Spatial Ecotypes from Single-Cell Gene Expression Data
        href: articles/Recovery_scRNA.html
      - text: Recovery of Spatial Ecotypes from Bulk Gene Expression Data
        href: articles/Recovery_Bulk.html

    - text: R functions
      href: reference/index.html
    - text: News
      href: news/index.html

reference:
- title: Discovery of spatial ecotypes (SEs)
  contents:
  - SpatialEcoTyper
  - MultiSpatialEcoTyper
  - IntegrateSpatialEcoTyper
  - GetSpatialMetacells
  - ComputeAvgs
  - SNF2
  - GetPCList
  - GetSNList
  - Integrate

- title: Development of SE recovery models
  desc:  Developing models for recovering spatial ecotypes from single-cell spatial data, scRNA-seq data, Visium spatial data, or bulk tumor expression data.
  contents:
  - CreatePseudobulks
  - NMFGenerateW
  - NMFGenerateWList

- title: SE recovery
  desc:  Recovering spatial ecotypes from single-cell spatial data, scRNA-seq data, Visium spatial data, or bulk tumor expression data.
  contents:
  - RecoverSE
  - DeconvoluteSE
  - NMFpredict

- title: NMF (Non-negative Matrix Factorization) clustering
  desc:  Clustering via NMF.
  contents:
  - nmfClustering

- title: Visualization
  contents:
  - SpatialView
  - HeatmapView
  - drawRectangleAnnotation
  - getColors

- title: Data processing
  contents:
  - PreprocessST
  - AnnotateCells
  - Znorm
  - rankSparse
  - matrixMultiply
  - fillspots
  - mostFrequent

news:
  releases:
  - text: "Version 1.0.0"
    href: