_pkgdown.yml

template:
  params:
    bootswatch: yeti

reference:
- title: Primary celda functions
  desc: Functions for clustering of cells
  contents:
  - celda_CG
  - celda_C
  - celda_G
  - reportCeldaCGRun
  - reportCeldaCGPlotResults
  - selectFeatures  
  - splitModule

- title: Visualization functions for celda results
  desc: Functions for displaying celda resuls on 2-D embeddings, heatmaps, and violin plots
  contents:
  - celdaUmap
  - celdaTsne
  - moduleHeatmap
  - celdaProbabilityMap
  - plotDimReduceCluster
  - plotDimReduceFeature
  - plotDimReduceModule
  - plotDimReduceGrid  
  - plotCeldaViolin  
  - celdaHeatmap

- title: Primary decontX functions
  desc: Functions for estimating and displaying contamination with decontX
  contents:
  - decontX
  - plotDecontXContamination
  - plotDecontXMarkerExpression
  - plotDecontXMarkerPercentage
  - decontXcounts
  
- title: Functions for determining the numbers of clusters in celda
  desc: Functions for running and comparing multiple celda models with different number of modules or cell populations
  contents:
  - recursiveSplitCell
  - recursiveSplitModule
  - plotRPC
  - celdaGridSearch
  - plotGridSearchPerplexity
  - perplexity
  - resamplePerplexity
  - selectBestModel
  - resList  
  - subsetCeldaList  
  - appendCeldaList
  - celdaPerplexity
  
- title: Miscellaneous celda functions 
  desc: Various functions for manipulation of celda results
  contents:
  - celdaClusters
  - celdaModules
  - recodeClusterY
  - recodeClusterZ
  - reorderCelda  
  - featureModuleLookup
  - featureModuleTable
  - celda
  - params  
  - runParams  
  - factorizeMatrix
  - bestLogLikelihood
  - clusterProbability
  - geneSetEnrich
  - plotHeatmap
  - retrieveFeatureIndex
  - normalizeCounts
  - distinctColors
  - matrixNames
  - logLikelihood
  - logLikelihoodHistory
  - topRank
  - sampleLabel

- title: Simulation functions
  desc: Functions for generating data from the generative process of each model 
  contents:
  - simulateCells
  - simulateContamination

- title: Data objects
  desc: Small data objects used in examples
  contents:
  - sceCeldaCG
  - sceCeldaC
  - sceCeldaG
  - sceCeldaCGGridSearch
  - celdaCGGridSearchRes
  - sampleCells
  - contaminationSim

- title: internal
  contents:
  - availableModels
  - celdaCGMod
  - celdaCGSim 
  - celdaCMod
  - celdaCSim
  - celdaGMod
  - celdaGSim
  - celdaModel
  - celdatosce
  - compareCountMatrix
  - countChecksum
  - eigenMatMultInt
  - eigenMatMultNumeric
  - fastNormProp
  - fastNormPropLog
  - fastNormPropSqrt
  - nonzero
  - semiPheatmap
  - '`celdaPerplexity,celdaList-method`'
  - '`countChecksum,celdaList-method`'
  
navbar:
  title: "celda"
  left:
    - icon: fa-home fa-lg
      href: https://www.camplab.net/celda
    - text: "Installation"
      href: articles/articles/installation.html
    - text: "Vignettes"
      menu:
      - text: "Celda - Analysis of PBMC3K"
        href: articles/articles/celda_pbmc3k.html
      - text: "DecontX - Decontamination of PBMC4K"
        href: articles/articles/decontX_pbmc4k.html
    - text: "Reference"
      href: reference/index.html
    - text: "News"
      href: news/index.html
    - icon: fa-github
      href: https://github.com/campbio/celda