_pkgdown.yml

template:
  params:
    bootstrap: 4
    bootswatch: cosmo
    ganalytics: G-BCXT5392QC

authors:
  Ruben Dries:
    href: https://www.drieslab.com/

title: Giotto Suite

navbar:
  title: ~
  type: default
  left:
    - text: "Start"
      menu:
      - text: "Installation"
        href: articles/getting_started.html#installation
      - text: "Getting Started"
        href: articles/getting_started.html#getting-started
      - text: "Analyses"
        href: articles/getting_started.html#analyses
    - text: "Documentation"
      href: reference/index.html
    - text: "Datasets"
      menu:
      - text: "Array based"
        href: articles/datasets_overview.html#array-based-datasets-1
      - text: "Single-cell"
        href: articles/datasets_overview.html#single-cell-1
      - text: "Subcellular"
        href: articles/datasets_overview.html#subcellular-datasets-1
      - text: "Protein multiplexing"
        href: articles/datasets_overview.html#protein-multiplexing-1
    - text: "Contribute"
      href: articles/contribute.html
    - text: "News"
      href: articles/giotto_news.html
    - text: "FAQ"
      menu:
        - text: Frequently Asked Questions
          href: articles/faqs.html
        - text: GitHub Issues Guidelines
          href: articles/github_issues.html
    - text: "Try Giotto"
      menu:
        - text: "Docker"
          href:
        - text: "Binder"
          href:


reference:
  - title: Giotto environment
    desc: install & work with Giotto python environment
    contents:
    - installGiottoEnvironment
    - removeGiottoEnvironment
    - checkGiottoEnvironment

  - title: Giotto instructions
    desc: Create or change Giotto instructions
    contents:
    - createGiottoInstructions
    - readGiottoInstructions
    - showGiottoInstructions
    - changeGiottoInstructions
    - replaceGiottoInstructions

  - title: Import raw data
    desc: functions to help to import raw spatial data
    contents:
    - getSpatialDataset
    - readExprMatrix
    - get10Xmatrix
    - get10Xmatrix_h5
    - stitchFieldCoordinates
    - stitchTileCoordinates

  - title: Images
    desc: functions to work with images for a Giotto object
    contents:
    - giottoImage
    - giottoLargeImage
    - createGiottoImage
    - createGiottoLargeImage
    - createGiottoLargeImageList
    - estimateImageBg
    - changeImageBg
    - addGiottoImageMG
    - addGiottoImageToSpatPlot
    - updateGiottoImageMG
    - stitchGiottoLargeImage
    - cropGiottoLargeImage
    - convertGiottoLargeImageToMG
    - writeGiottoLargeImage
    - updateGiottoLargeImage
    - addGiottoLargeImage
    - plotGiottoImage
    - addGiottoImage
    - updateGiottoImage
    - reconnectGiottoImage
    - showGiottoImageNames

  - title: Image registration
    desc: functions to work with fiji images
    contents:
    - registerGiottoObjectList
    - registerGiottoObjectListFiji
    - registerGiottoObjectListRvision
    - registerImagesFIJI
    - fiji

  - title: Giotto object
    desc: Create Giotto objects
    contents:
    - createGiottoObject
    - createGiottoVisiumObject
    - createGiottoObjectSubcellular

  - title: Giotto helper functions
    desc: Common functions to help working with Giotto objects
    contents:
    - pDataDT
    - fDataDT
    - filterDistributions
    - filterCombinations
    - showProcessingSteps
    - calculateMetaTable
    - calculateMetaTableCells
    - combineMetadata
    - createMetafeats
    - findNetworkNeighbors
    - combineSpatialCellFeatureInfo
    - combineSpatialCellMetadataInfo
    - getDistinctColors
    - stitchFieldCoordinates
    - stitchTileCoordinates
    - convertEnsemblToGeneSymbol
    - readPolygonFilesVizgenHDF5
    - readPolygonFilesVizgen


  - title: Giotto getters & setters
    desc: Low level functions to get, set and show Giotto slots
    contents:
    - get_expression_values
    - set_expression_values
    - get_spatial_locations
    - set_spatial_locations
    - get_dimReduction
    - set_dimReduction
    - get_NearestNetwork
    - set_NearestNetwork
    - get_spatialNetwork
    - set_spatialNetwork
    - get_spatialGrid
    - set_spatialGrid
    - get_polygon_info
    - set_polygon_info
    - get_feature_info
    - set_feature_info
    - get_spatial_enrichment
    - set_spatial_enrichment
    - getSpatialDataset
    - list_expression
    - list_expression_names
    - list_spatial_locations
    - list_spatial_locations_names
    - list_spatial_enrichments
    - list_spatial_enrichments_names
    - list_dim_reductions
    - list_dim_reductions_names
    - list_spatial_info
    - list_spatial_info_names
    - list_feature_info
    - list_feature_info_names
    - list_spatial_networks
    - list_spatial_networks_names
    - list_spatial_grids
    - list_spatial_grids_names
    - list_image_names
    - get10Xmatrix
    - get10Xmatrix_h5

  - title: Giotto show slots
    desc: Show what is available in different information slots
    contents:
    - showGiottoExpression
    - showGiottoSpatLocs
    - showGiottoSpatEnrichments
    - showGiottoDimRed
    - showGiottoSpatialInfo
    - showGiottoFeatInfo
    - showGiottoSpatNetworks
    - showGiottoSpatGrids

  - title: Modify Giotto object
    desc: Modifications to the Giotto objects
    contents:
    - filterGiotto
    - subsetGiotto
    - subsetGiottoLocs
    - subsetGiottoLocsMulti
    - joinGiottoObjects
    - normalizeGiotto
    - adjustGiottoMatrix
    - processGiotto
    - annotateGiotto
    - removeCellAnnotation
    - removeFeatAnnotation
    - addCellMetadata
    - addFeatMetadata
    - addFeatStatistics
    - addCellStatistics
    - addStatistics
    - addFeatsPerc
    - addCellIntMetadata

  - title: dimension reduction
    desc: Functions to reduce dimensions
    contents:
    - calculateHVF
    - signPCA
    - screePlot
    - jackstrawPlot
    - runPCA
    - runUMAP
    - runtSNE
    - runGiottoHarmony

  - title: Clustering
    desc: Functions to cluster cells
    contents:
    - doLeidenCluster
    - doLouvainCluster
    - doRandomWalkCluster
    - doSNNCluster
    - doKmeans
    - doHclust
    - clusterCells
    - doLeidenSubCluster
    - doLouvainSubCluster
    - subClusterCells
    - getClusterSimilarity
    - mergeClusters
    - getDendrogramSplits
    - createNearestNetwork
    - addNetworkLayout

  - title: Marker genes
    desc: Functions to detect cell type / cluster specific marker genes
    contents:
    - findMarkers
    - findMarkers_one_vs_all
    - findGiniMarkers
    - findGiniMarkers_one_vs_all
    - findScranMarkers
    - findScranMarkers_one_vs_all
    - findMastMarkers
    - findMastMarkers_one_vs_all

  - title: Auxiliary visualizations
    desc: Different visualization options to explore gene, cell or cluster characteristics
    contents:
    - showSaveParameters
    - showClusterHeatmap
    - showClusterDendrogram
    - plotHeatmap
    - plotMetaDataHeatmap
    - plotMetaDataCellsHeatmap
    - violinPlot

  - title: Spatial structures
    desc: functions to setup spatial structures
    contents:
    - spatNetwDistributionsDistance
    - spatNetwDistributionsKneighbors
    - spatNetwDistributions
    - createSpatialDelaunayNetwork
    - plotStatDelaunayNetwork
    - createSpatialKNNnetwork
    - createSpatialNetwork
    - annotateSpatialNetwork
    - createSpatialDefaultGrid
    - createSpatialGrid
    - annotateSpatialGrid

  - title: Spatial enrichment
    desc: algorithms to compute spatial enrichment of gene signatures or scRNA-seq matrix
    contents:
    - makeSignMatrixPAGE
    - makeSignMatrixDWLSfromMatrix
    - makeSignMatrixDWLS
    - makeSignMatrixRank
    - runPAGEEnrich_OLD
    - runPAGEEnrich
    - PAGEEnrich
    - runRankEnrich
    - rankEnrich
    - runHyperGeometricEnrich
    - hyperGeometricEnrich
    - runSpatialEnrich
    - createSpatialEnrich
    - runDWLSDeconv
    - runSpatialDeconv

  - title: Spatial deconvolution
    desc: algorithms to perform spatial deconvolution based on gene signatures or single-cell RNAseq information
    contents:
    - makeSignMatrixDWLSfromMatrix
    - makeSignMatrixDWLS
    - runSpatialDeconv
    - runDWLSDeconv

  - title: Spatial network or grid
    desc: Function to (help) create a spatial network or grid
    contents:
    - spatNetwDistributionsDistance
    - spatNetwDistributionsKneighbors
    - spatNetwDistributions
    - createSpatialDelaunayNetwork
    - plotStatDelaunayNetwork
    - createSpatialKNNnetwork
    - createSpatialNetwork
    - annotateSpatialNetwork
    - annotateSpatialGrid
    - createSpatialGrid

  - title: Spatial Expression Patterns
    desc: Methods to detect spatially coherent expression patterns
    contents:
    - binSpectSingleMatrix
    - binSpectSingle
    - binSpectMulti
    - binSpectMultiMatrix
    - binSpect
    - silhouetteRank
    - silhouetteRankTest
    - spatialDE
    - spatialAEH
    - trendSceek
    - spark
    - detectSpatialPatterns
    - showPattern2D
    - showPattern
    - showPattern3D
    - showPatternGenes
    - selectPatternGenes

  - title: Simulate spatial expression patterns
    desc: Function to simulate a user-defined pattern using the full complexity of the different gene distributions.
    contents:
    - simulateOneGenePatternGiottoObject
    - runPatternSimulation

  - title: Spatial Co-Expression Modules
    desc: Method to detect spatially co-expressed feature modules
    contents:
    - ends_with("SpatialCorFeats")
    - detectSpatialCorFeatsMatrix
    - detectSpatialCorFeats
    - showSpatialCorFeats
    - clusterSpatialCorFeats
    - heatmSpatialCorFeats
    - rankSpatialCorGroups

  - title: Spatial in situ visuals
    desc: Functions for spatial in situ visualization
    contents:
    - spatInSituPlotDensity
    - spatInSituPlotHex
    - spatInSituPlotPoints

  - title: Spatial interaction visuals
    desc: Functions for spatial interaction visualization
    contents:
    - cellProximityBarplot
    - cellProximityHeatmap
    - cellProximityNetwork
    - cellProximityVisPlot
    - plotCellProximityGenes
    - combineCPG
    - plotInteractionChangedGenes
    - plotICG
    - plotCombineInteractionChangedGenes
    - plotCombineCellProximityGenes
    - plotCombineICG
    - plotCombineCPG
    - plotCombineCellCellCommunication
    - plotCombineCCcom
    - plotCCcomHeatmap
    - cellProximitySpatPlot
    - cellProximitySpatPlot3D
    - plotCPG

  - title: HMRF
    desc: Functions to identify spatial domains with HMRF
    contents:
    - doHMRF
    - loadHMRF
    - viewHMRFresults
    - writeHMRFresults
    - addHMRF
    - viewHMRFresults2D
    - viewHMRFresults3D

  - title: 2D visualization in expression space
    desc: Visualization of expression space (e.g. UMAP) in 2D
    contents:
    - dimPlot
    - dimPlot2D
    - plotUMAP_2D
    - plotUMAP
    - plotTSNE_2D
    - plotTSNE
    - plotPCA_2D
    - plotPCA
    - dimFeatPlot2D
    - dimCellPlot2D
    - dimCellPlot

  - title: 2D visualization in spatial space
    desc: Visualization in 2D spatial space
    contents:
    - spatPlot2D
    - spatPlot
    - spatFeatPlot2D_single
    - spatFeatPlot2D
    - spatCellPlot2D
    - spatCellPlot

  - title: 2D visualization in spatial and expression space
    desc: Visualization in both 2D spatial and expression space
    contents:
    - spatDeconvPlot
    - spatDimPlot2D
    - spatDimPlot
    - spatDimFeatPlot2D
    - spatDimCellPlot2D
    - spatDimCellPlot

  - title: 3D dimension reduction visualization
    desc: Visualization of expression space (e.g. UMAP) in 3D
    contents:
    - dimPlot3D
    - plotUMAP_3D
    - plotTSNE_3D
    - plotPCA_3D
    - dimGenePlot3D

  - title: 3D visualization in spatial space
    desc: Visualization in 3D spatial space
    contents:
    - spatPlot3D

  - title: 3D visualization in spatial and expression space
    desc: Visualization in both 3D spatial and expression space
    contents:
    - spatDimPlot3D
    - spatGenePlot3D
    - spatDimGenePlot3D

  - title: In silico cross sections
    desc: create in silico 2D cross sections from 3D data
    contents:
    - create_crossSection_object
    - createCrossSection
    - crossSectionGenePlot
    - crossSectionPlot
    - crossSectionGenePlot3D
    - crossSectionPlot3D
    - insertCrossSectionSpatPlot3D
    - insertCrossSectionGenePlot3D

  - title: cell neighborhood; cell-type/cell-type enrichment
    desc: calculate and visualize cell-type/cell-type spatial enrichment or depletion
    contents:
    - cellProximityEnrichment
    - cellProximityBarplot
    - cellProximityHeatmap
    - cellProximityNetwork
    - cellProximitySpatPlot
    - cellProximitySpatPlot3D

  - title: cell neighborhood; spatial interaction changed genes
    desc: Identify and visualize genes that change in a source cell type due to interaction with another neighboring cell type
    contents:
    - findInteractionChangedFeats
    - findICF
    - filterInteractionChangedFeats
    - filterICF
    - combineInteractionChangedGenes
    - combineICG
    - plotInteractionChangedGenes
    - plotICG
    - plotCombineInteractionChangedGenes
    - plotCombineICG

  - title: cell neighborhood; ligand-receptor cell communication
    desc: Find putative increased spatial ligand-receptor activity between cells of pairs of cell types
    contents:
    - exprCellCellcom
    - specificCellCellcommunicationScores
    - spatCellCellcom
    - combCCcom
    - plotCCcomDotplot
    - plotRankSpatvsExpr
    - plotRecovery
    - plotRecovery_sub

  - title: Cell segmentation
    desc: Functions for cell segmentation
    contents:
    - doCellSegmentation

  - title: Interoperability
    desc: Convert other type of objects into a Giotto object
    contents:
    - seuratToGiotto

  - title: Giotto structures
    desc: General Giotto object structure
    contents:
    - giottoPolygon
    - createGiottoPolygonsFromMask
    - createGiottoPolygonsFromDfr
    - addGiottoPolygons
    - smoothGiottoPolygons
    - giottoPoints
    - featureNetwork
    - createGiottoPoints
    - addGiottoPoints
    - createSpatialFeaturesKNNnetwork
    - addSpatialCentroidLocationsLayer
    - addSpatialCentroidLocations
    - calculateOverlapRaster
    - calculateOverlapSerial
    - calculateOverlapParallel
    - overlapToMatrix
    - overlapToMatrixMultiPoly
    - combineCellData
    - combineFeatureData
    - combineFeatureOverlapData

  - title: Interactive selection
    desc: Interactive selection of cells and transcripts
    contents:
    - plotInteractivePolygons

  - title: Python scrublet
    desc: Run scrublet doublet detection for raw expression.
    contents:
    - doScrubletDetect

  - title: Giotto viewer
    desc: Export Giotto object to Giotto viewer format.
    contents:
    - exportGiottoViewer

  - title: mini Giotto
    desc: mini Giotto objects
    contents:
    - mini_giotto_3D
    - mini_giotto_multi_cell
    - mini_giotto_single_cell
    - giotto-class
    - show,giotto-method