From a559e86c03813122f6de56c7ed7545cc0d95e73d Mon Sep 17 00:00:00 2001 From: Joselyn Chavez Date: Mon, 18 Dec 2023 14:06:26 -0600 Subject: [PATCH] add references order and update tutorials --- _pkgdown.yml | 699 ++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 658 insertions(+), 41 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 3d3c02cb1..f1254e538 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,12 +1,16 @@ url: https://drieslab.github.io/Giotto/ authors: - Joselyn Chávez: + Ruben Dries: + href: https://www.drieslab.com + Guo-Cheng Yuan: + href: https://labs.icahn.mssm.edu/yuanlab/ + Joselyn C. Chávez-Fuentes: href: https://josschavezf.github.io template: - bootstrap: 5 + bootstrap: 3 bslib: bg: "#FFFFFF" fg: "#000000" @@ -17,91 +21,218 @@ development: mode: auto navbar: - bg: dark + bg: light structure: left: - intro + - get_started - reference - articles + - tools - news right: - search - github components: + get_started: + text: Get started + menu: + - text: Giotto Installation + href: articles/installation.html + - text: Giotto Ecosystem + href: articles/ecosystem.html + - text: Giotto Class Structure + href: articles/structure.html + - text: Solutions to Installation Errors + href: articles/errorsfaqsandtips.html + - text: FAQs + href: articles/faqs.html + - text: Branches + href: articles/branches.html + - text: How to report a bug + href: articles/github_issues.html reference: text: Documentation href: reference/index.html - articles: + tools: text: Tutorials menu: + - text: Giotto Object Creation + href: articles/object_creation.html + - text: ------- + - text: Giotto Configuration + href: articles/configuration.html + - text: ------- + - text: Spatial manipulation + - text: Spatial transformations + href: articles/spatial_transformations.html + - text: ------- + - text: Image alignment + - text: Image alignment + href: articles/image_alignment.html + - text: ------- + - text: Interactive selection + - text: Interactive selection + href: articles/interactive_selection.html + - text: ------- + - text: Visualizations + - text: Visualizations + href: articles/visualizations.html + - text: ------- + - text: Saving and Loading + - text: Saving a Giotto object + href: articles/saving_object.html + - text: Saving plots + href: articles/saving_plots.html + - text: ------- + - text: Interoperability + - text: AnnData + href: articles/interoperability_anndata.html + - text: ------- + - text: Try Giotto in the Cloud + - text: Terra.bio + href: articles/terra.html + - text: Docker + href: articles/docker.html + articles: + text: Examples + menu: - text: Seq-Scope - - text: Mouse liver - href: articles/seqscope_mouse_liver.html + menu: + - text: Mouse liver + href: articles/seqscope_mouse_liver.html - text: ------- - text: Visium - - text: Visium Mouse Kidney - href: articles/visium_mouse_kidney.html - - text: Visium Mouse Brain - href: articles/visium_mouse_brain.html - - text: Visium Prostate Integration - href: articles/visium_prostate_integration.html - - text: CytAssist Human Lung Cancer - href: articles/visium_cytassist_lungcancer.html - - text: CytAssist Multi-omics Human Glioblastoma - href: articles/visium_cytassist_human_glioblastoma.html + menu: + - text: Visium Mouse Kidney + href: articles/visium_mouse_kidney.html + - text: Visium Mouse Brain + href: articles/visium_mouse_brain.html + - text: Visium Prostate Integration + href: articles/visium_prostate_integration.html + - text: CytAssist Human Lung Cancer + href: articles/visium_cytassist_lungcancer.html + - text: CytAssist Multi-omics Human Glioblastoma + href: articles/visium_cytassist_human_glioblastoma.html - text: ------- - text: Spatial Genomics - - text: Mouse Kidney - href: articles/spatial_genomics_mouse_kidney.html + menu: + - text: Mouse Kidney + href: articles/spatial_genomics_mouse_kidney.html - text: ------- - text: Xenium - - text: Xenium Human breast cancer - href: articles/xenium_breast_cancer.html + menu: + - text: Xenium Human breast cancer + href: articles/xenium_breast_cancer.html - text: ------- - text: Nanostring CosMx - - text: Nanostring CosMx Subcellular Lung Cancer - href: articles/nanostring_cosmx_lung_cancer.html + menu: + - text: Nanostring CosMx Subcellular Lung Cancer + href: articles/nanostring_cosmx_lung_cancer.html - text: ------- - text: MERFISH - - text: MERFISH Mouse Hypothalamic Preoptic Region - href: articles/merfish_mouse_hypothalamic.html + menu: + - text: MERFISH Mouse Hypothalamic Preoptic Region + href: articles/merfish_mouse_hypothalamic.html - text: ------- - text: Vizgen - - text: Vizgen Mouse Brain Receptor Map - href: articles/vizgen_mouse_brain.html + menu: + - text: Vizgen Mouse Brain Receptor Map + href: articles/vizgen_mouse_brain.html - text: ------- - text: seqFISH - - text: mini seqFISH - href: articles/mini_seqfish.html - - text: SeqFish+ Mouse Cortex Example - href: articles/seqfish_cortex.html + menu: + - text: mini seqFISH + href: articles/mini_seqfish.html + - text: SeqFish+ Mouse Cortex Example + href: articles/seqfish_cortex.html - text: ------- - text: osmFISH - - text: osmFISH Mouse SS Cortex - href: articles/osmfish_mouse_ss_cortex.html + menu: + - text: osmFISH Mouse SS Cortex + href: articles/osmfish_mouse_ss_cortex.html - text: ------- - text: Resolve Bioscience - - text: Resolve Bioscience Breast Cancer Subcellular - href: articles/resolve_biosciences.html + menu: + - text: Resolve Bioscience Breast Cancer Subcellular + href: articles/resolve_biosciences.html - text: ------- - text: CODEX - - text: Codex Mouse Spleen - href: articles/codex_mouse_spleen.html + menu: + - text: Codex Mouse Spleen + href: articles/codex_mouse_spleen.html - text: ------- - text: Single Cell RNA Sequencing - - text: Prostate - href: articles/singlecell_prostate_standard.html - - text: Prostate Integration - href: articles/singlecell_prostate_integration.html + menu: + - text: Prostate + href: articles/singlecell_prostate_standard.html + - text: Prostate Integration + href: articles/singlecell_prostate_integration.html news: text: News - href: news/index.html + menu: + - text: Changes + href: news/index.html + - text: Presentations + href: articles/presentations.html github: icon: fab fa-github fa-lg href: https://github.com/drieslab/Giotto/ aria-label: github articles: +- title: News + navbar: ~ + contents: + - presentations +- title: Get started + navbar: ~ + contents: + - installation + - ecosystem + - structure + - errorsfaqsandtips + - faqs + - branches + - github_issues +- title: Giotto Object Creation + navbar: ~ + contents: + - object_creation +- title: Giotto Configuration + navbar: ~ + contents: + - configuration +- title: Try Giotto in the Cloud + navbar: ~ + contents: + - terra + - docker +- title: Spatial Manipulation + navbar: ~ + contents: + - spatial_transformations +- title: Image alignment + navbar: ~ + contents: + - image_alignment +- title: Interactive selection + navbar: ~ + contents: + - interactive_selection +- title: Visualizations + navbar: ~ + contents: + - visualizations +- title: Saving and Loading + navbar: ~ + contents: + - saving_object + - saving_plots +- title: Interoperability + navbar: ~ + contents: + - interoperability_anndata - title: Seq-Scope navbar: ~ contents: @@ -164,3 +295,489 @@ news: home: sidebar: structure: [links, license, community, citation, authors, dev] + +reference: +- title: Giotto Environment + desc: Install and work with Giotto Python Environment. +- contents: + - GiottoClass::installGiottoEnvironment + - GiottoClass::removeGiottoEnvironment + - GiottoClass::checkGiottoEnvironment +- title: Giotto Instructions + desc: Create or change Giotto instructions. +- contents: + - GiottoClass::createGiottoInstructions + - GiottoClass::readGiottoInstructions + - GiottoClass::changeGiottoInstructions + - GiottoClass::replaceGiottoInstructions +- title: Import Raw Data + desc: Functions to help to import raw spatial data. +- contents: + - GiottoData::getSpatialDataset + - GiottoClass::readExprMatrix + - get10Xmatrix + - get10XmatrixOLD + - get10Xmatrix_h5 + - GiottoClass::stitchFieldCoordinates + - GiottoClass::stitchTileCoordinates + - readPolygonFilesVizgen + - readPolygonFilesVizgenHDF5 + - getGEFtxCoords +- title: Images + desc: Functions to work with images for a Giotto object. +- contents: + - GiottoClass::estimateImageBg + - GiottoClass::changeImageBg + - GiottoClass::createGiottoImage + - GiottoClass::addGiottoImage + - GiottoVisuals::addGiottoImageToSpatPlot + - GiottoClass::showGiottoImageNames + - GiottoClass::updateGiottoImage + - GiottoClass::getGiottoImage + - GiottoClass::plotGiottoImage + - GiottoClass::setGiottoImage + - GiottoClass::addGiottoLargeImage + - GiottoClass::createGiottoLargeImage + - GiottoClass::createGiottoLargeImageList + - createMerscopeLargeImage + - GiottoClass::cropGiottoLargeImage + - GiottoClass::updateGiottoLargeImage + - GiottoClass::writeGiottoLargeImage + - GiottoClass::stitchGiottoLargeImage + - GiottoClass::convertGiottoLargeImageToMG + - GiottoClass::addGiottoImageMG + - GiottoClass::updateGiottoImageMG + - GiottoClass::distGiottoImage + - GiottoClass::reconnectGiottoImage + - registerImagesFIJI + - registerGiottoObjectList + - registerGiottoObjectListFiji + - registerGiottoObjectListRvision +- title: Giotto Object + desc: Functions to help to import raw spatial data. +- contents: + - GiottoClass::createGiottoObject + - createGiottoVisiumObject + - GiottoClass::createGiottoObjectSubcellular + - createGiottoCosMxObject + - createGiottoMerscopeObject + - createGiottoObjectfromArchR + - createArchRProj + - createGiottoXeniumObject + - readPolygonFilesVizgenHDF5_old +- title: Giotto Helper Functions + desc: Common functions to help working with Giotto objects. +- contents: + - GiottoClass::pDataDT + - GiottoClass::fDataDT + - GiottoClass::showProcessingSteps + - GiottoClass::calculateMetaTable + - GiottoClass::calculateMetaTableCells + - GiottoClass::combineMetadata + - GiottoClass::createMetafeats + - findNetworkNeighbors + - GiottoClass::objHistory + - fiji +- title: Giotto Getters & Setters + desc: Low level functions to get, set and show Giotto slots. +- contents: + - GiottoClass::getExpression + - GiottoClass::setExpression + - GiottoClass::getSpatialLocations + - GiottoClass::setSpatialLocations + - GiottoClass::getDimReduction + - GiottoClass::setDimReduction + - GiottoClass::getNearestNetwork + - GiottoClass::setNearestNetwork + - GiottoClass::getSpatialNetwork + - GiottoClass::setSpatialNetwork + - GiottoClass::getSpatialGrid + - GiottoClass::setSpatialGrid + - GiottoClass::getPolygonInfo + - GiottoClass::setPolygonInfo + - GiottoClass::getFeatureInfo + - GiottoClass::setFeatureInfo + - GiottoClass::getFeatureMetadata + - GiottoClass::setFeatureMetadata + - GiottoClass::getSpatialEnrichment + - GiottoClass::setSpatialEnrichment + - GiottoClass::getCellMetadata + - GiottoClass::setCellMetadata + - GiottoClass::getMultiomics + - GiottoClass::setMultiomics +- title: Giotto Show Slots + desc: Show what is available in different information slots. +- contents: + - GiottoClass::showGiottoExpression + - GiottoClass::showGiottoCellMetadata + - GiottoClass::showGiottoDimRed + - GiottoClass::showGiottoFeatInfo + - GiottoClass::showGiottoFeatMetadata + - GiottoClass::showGiottoImageNames + - GiottoClass::showGiottoInstructions + - GiottoClass::showGiottoNearestNetworks + - GiottoClass::showGiottoSpatEnrichments + - GiottoClass::showGiottoSpatGrids + - GiottoClass::showGiottoSpatialInfo + - GiottoClass::showGiottoSpatLocs + - GiottoClass::showGiottoSpatNetworks + - GiottoClass::showGrids + - GiottoClass::showNetworks + - showPattern + - showPattern2D + - showPattern3D + - showPatternGenes +- title: Modify Giotto Object + desc: Modifications to the Giotto objects. +- contents: + - filterGiotto + - filterCombinations + - filterDistributions + - GiottoClass::subsetGiotto + - GiottoClass::subsetGiottoLocs + - GiottoClass::subsetGiottoLocsMulti + - GiottoClass::joinGiottoObjects + - normalizeGiotto + - adjustGiottoMatrix + - GiottoClass::annotateGiotto + - GiottoClass::removeCellAnnotation + - GiottoClass::removeFeatAnnotation + - GiottoClass::addCellMetadata + - GiottoClass::addFeatMetadata + - addFeatStatistics + - addCellStatistics + - addStatistics + - addFeatsPerc + - addCellIntMetadata + - processGiotto + - filterCPG +- title: Dimension Reduction + desc: Functions to reduce dimensions. +- contents: + - calculateHVF + - signPCA + - screePlot + - create_screeplot + - jackstrawPlot + - runPCA + - runUMAP + - runtSNE + - runGiottoHarmony + - runWNN + - runIntegratedUMAP + - runPCAprojection + - runPCAprojectionBatch + - runUMAPprojection +- title: Clustering + desc: Functions to cluster cells. +- contents: + - calculateHVF + - GiottoClass::createNearestNetwork + - GiottoClass::addNetworkLayout + - clusterCells + - doLeidenCluster + - doLeidenClusterIgraph + - doLouvainCluster + - doKmeans + - doHclust + - doRandomWalkCluster + - doSNNCluster + - subClusterCells + - doLeidenSubCluster + - doLouvainSubCluster + - getClusterSimilarity + - mergeClusters + - getDendrogramSplits + - doClusterProjection + - doGiottoClustree +- 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: Functions for different visualization options to explore gene, cell or cluster characteristics. +- contents: + - GiottoVisuals::showClusterHeatmap() + - GiottoVisuals::showClusterDendrogram + - GiottoVisuals::plotHeatmap + - GiottoVisuals::plotMetaDataHeatmap + - GiottoVisuals::plotMetaDataCellsHeatmap + - GiottoVisuals::violinPlot + - callSpdep +- title: Spatial Enrichment + desc: Algorithms to compute spatial enrichment of gene signatures or scRNA-seq matrix. +- contents: + - makeSignMatrixPAGE + - makeSignMatrixRank + - runSpatialEnrich + - runPAGEEnrich + - runPAGEEnrich_OLD + - runRankEnrich + - rankEnrich + - runHyperGeometricEnrich + - hyperGeometricEnrich + - PAGEEnrich + - createSpatialEnrich + - createSpatialGenomicsObject + - doFeatureSetEnrichment + - selectPatternGenes + - silhouetteRank + - silhouetteRankTest +- title: Spatial Deconvolution + desc: Algorithms to perform spatial deconvolution based on gene signatures or single-cell RNAseq information. +- contents: + - makeSignMatrixDWLSfromMatrix + - makeSignMatrixDWLS + - runSpatialDeconv + - runDWLSDeconv + - GiottoVisuals::spatDeconvPlot + - featExpDWLS +- title: Spatial Network or Grid + desc: Function to (help) create a spatial network or grid. +- contents: + - GiottoVisuals::spatNetwDistributionsDistance + - GiottoVisuals::spatNetwDistributionsKneighbors + - GiottoVisuals::spatNetwDistributions + - GiottoClass::createSpatialDelaunayNetwork + - GiottoVisuals::plotStatDelaunayNetwork + - GiottoClass::createSpatialKNNnetwork + - GiottoClass::annotateSpatialNetwork + - GiottoClass::annotateSpatialGrid + - GiottoClass::createSpatialGrid + - GiottoClass::createSpatialDefaultGrid +- title: Spatial Expression Patterns + desc: Methods to detect spatially coherent expression patterns. +- contents: + - binSpectSingleMatrix + - binSpectSingle + - binSpectMultiMatrix + - binSpectMulti + - binSpect + - spatialDE + - spatialAEH + - trendSceek + - spark + - filterSpatialGenes +- 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: + - clusterSpatialCorFeats + - detectSpatialCorFeats + - detectSpatialCorGenes + - clusterSpatialCorGenes + - detectSpatialCorFeatsMatrix + - detectSpatialPatterns + - heatmSpatialCorFeats + - heatmSpatialCorGenes + - showSpatialCorFeats + - showSpatialCorGenes + - rankSpatialCorGroups + - getBalancedSpatCoexpressionFeats +- title: Spatial Data Handling + desc: Functions to condense spatial data. +- contents: + - GiottoClass::combineSpatialCellFeatureInfo + - GiottoClass::combineSpatialCellMetadataInfo +- title: Hidden Markov Random Field (HMRF) + desc: Functions to identify spatial domains with HMRF. +- contents: + - doHMRF + - doHMRF_V2 + - initHMRF_V2 + - loadHMRF + - viewHMRFresults + - viewHMRFresults_V2 + - writeHMRFresults + - addHMRF + - addHMRF_V2 + - viewHMRFresults + - viewHMRFresults2D + - viewHMRFresults3D +- title: General Plotting + desc: Functions to assist in plotting. +- contents: + - GiottoVisuals::getDistinctColors + - GiottoVisuals::showSaveParameters +- title: 2D Visualization In Expression Space + desc: Visualization of expression space (e.g. UMAP) in 2D. +- contents: + - GiottoVisuals::dimPlot + - GiottoVisuals::dimPlot2D + - GiottoVisuals::plotUMAP + - GiottoVisuals::plotUMAP_2D + - GiottoVisuals::plotTSNE + - GiottoVisuals::plotTSNE_2D + - GiottoVisuals::plotPCA + - GiottoVisuals::plotPCA_2D + - GiottoVisuals::dimFeatPlot2D + - GiottoVisuals::dimCellPlot2D +- title: 2D Visualization in Spatial Space + desc: Visualization of expression space (e.g. UMAP) in 2D. +- contents: + - GiottoVisuals::spatPlot2D + - GiottoVisuals::spatCellPlot2D + - GiottoVisuals::spatFeatPlot2D +- title: 2D Visualization In Both Spatial And Expression Space + desc: Visualization in both 2D spatial and expression space. +- contents: + - GiottoVisuals::spatDimPlot2D + - GiottoVisuals::spatDimCellPlot2D + - GiottoVisuals::spatDimFeatPlot2D +- title: 3D Visualization Dimension Reduction + desc: Visualization of expression space (e.g. UMAP) in 3D. +- contents: + - GiottoVisuals::dimPlot3D + - GiottoVisuals::plotTSNE_3D + - GiottoVisuals::plotPCA_3D +- title: 3D Visualization In Spatial Space + desc: Visualization in 3D spatial space. +- contents: + - GiottoVisuals::spatPlot3D +- title: 3D visualization in Spatial and Expression Space + desc: Visualization in 3D spatial space. +- contents: + - GiottoVisuals::spatDimPlot3D +- title: In Silico Cross Sections + desc: Functions to create an in silico 2D cross sections from 3D data. +- contents: + - createCrossSection + - crossSectionGenePlot + - crossSectionPlot + - crossSectionGenePlot3D + - crossSectionPlot3D + - insertCrossSectionGenePlot3D + - insertCrossSectionSpatPlot3D + - create_crossSection_object +- title: Cell Neighborhood, Cell-Type/Cell-Type Enrichment + desc: Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion. +- contents: + - cellProximityEnrichment + - cellProximityEnrichmentEachSpot + - cellProximityEnrichmentSpots + - cellProximityBarplot + - cellProximityHeatmap + - cellProximityNetwork + - cellProximitySpatPlot + - cellProximitySpatPlot3D + - specificCellCellcommunicationScores + - filterCellProximityGenes + - findCellProximityGenes + - findCellTypesFromEnrichment + - pieCellTypesFromEnrichment + - plotCellTypesFromEnrichment + - plotCellProximityFeatSpot + - showCellProportionSwitchedPie + - showCellProportionSwitchedSanKey + - spatCellCellcomSpots +- title: Cell Neighborhood, Spatial Interaction Changed Features (ICF) + desc: Identify and visualize features (genes) that change in a source cell type due to interaction with another neighboring cell type. +- contents: + - findInteractionChangedFeats + - findICF + - findICFSpot + - findICG + - findCPG + - filterInteractionChangedFeats + - filterInteractionChangedGenes + - filterICF + - filterICFSpot + - filterICG + - plotICF + - plotICFSpot + - plotCellProximityFeats + - plotCPF + - combineInteractionChangedFeats + - combineICF + - plotCombineInteractionChangedFeats + - plotInteractionChangedFeats + - plotCombineICF + - combineCPG + - combineCellProximityGenes + - combineICG + - combineInteractionChangedGenes + - findInteractionChangedGenes + - spatialAutoCor + - spdepAutoCorr + - spatialSplitCluster +- title: Cell Neighborhood, Ligand-Receptor Cell Communication + desc: Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion. +- contents: + - combCCcom + - exprCellCellcom + - spatCellCellcom + - plotCCcomDotplot + - plotRankSpatvsExpr + - plotRecovery + - plotCCcomHeatmap + - plotCombineCellCellCommunication + - plotCombineCCcom +- title: Subcellular + desc: Functions to manipulate and visualize subcellular data. +- contents: + - addPolygonCells + - GiottoClass::addGiottoPoints + - GiottoClass::addGiottoPoints3D + - GiottoClass::addGiottoPolygons + - addVisiumPolygons + - GiottoClass::addSpatialCentroidLocations + - GiottoClass::addSpatialCentroidLocationsLayer + - GiottoClass::calculateOverlapParallel + - GiottoClass::calculateOverlapPolygonImages + - GiottoClass::calculateOverlapRaster + - GiottoClass::calculateOverlapSerial + - GiottoClass::combineCellData + - GiottoClass::combineFeatureData + - GiottoClass::combineFeatureOverlapData + - GiottoClass::createGiottoPoints + - GiottoClass::createGiottoPolygonsFromDfr + - GiottoClass::createGiottoPolygonsFromMask + - GiottoClass::overlapToMatrix + - GiottoClass::overlapImagesToMatrix + - GiottoClass::overlapToMatrixMultiPoly + - GiottoClass::smoothGiottoPolygons + - GiottoVisuals::spatInSituPlotDensity + - GiottoVisuals::spatInSituPlotHex + - GiottoVisuals::spatInSituPlotPoints + - showPolygonSizeInfluence +- title: Segmentation + desc: Function to segment cells in-tissue. +- contents: + - doCellSegmentation +- title: Doublet Detection + desc: Function to detect doublets in raw expression data. +- contents: + - doScrubletDetect +- title: Interactive Visualizations + desc: +- contents: + - cellProximitySpatPlot2D + - cellProximityVisPlot + - comparePolygonExpression + - getCellsFromPolygon + - plotInteractivePolygons + - plotPolygons + - plotInteractive3D + - compareCellAbundance + - exportGiottoViewer +- title: Interoperability + desc: Convert other type of objects into a Giotto object and vice versa. +- contents: + - GiottoClass::seuratToGiotto + - GiottoClass::giottoToSeurat + - GiottoClass::giottoToSpatialExperiment + - GiottoClass::giottoToAnnData + - GiottoClass::anndataToGiotto + - GiottoClass::giottoMasterToSuite + - convertEnsemblToGeneSymbol