Function Documentation¶
Giotto Environment¶
Install and work with Giotto Python Environment
Function |
Description |
|---|---|
installGiottoEnvironment |
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removeGiottoEnvironment |
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checkGiottoEnvironment |
Giotto Instructions¶
Create or change Giotto instructions
Function |
Description |
|---|---|
createGiottoInstructions |
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readGiottoInstrunctions |
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changeGiottoInstructions |
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changeGiottoInstructions |
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replaceGiottoInstructions |
Import Raw Data¶
Functions to help to import raw spatial datat
Function |
Description |
|---|---|
getSpatialDataset |
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readExprMatrix |
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get10Xmatrix |
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get10Xmatrix_h5 |
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stitchFieldCoordinates |
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stitchTileCoordinates |
Images¶
Functions to work with images for a Giotto object.
Function |
Description |
|---|---|
estimateImageBg |
|
changeImageBg |
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createGiottoImage |
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addGiottoImage |
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addGiottoImageToSpatPlot |
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showGiottoImageNames |
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updateGiottoImage |
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getGiottoImage |
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plotGiottoImage |
Giotto Object¶
Functions to help to import raw spatial data.
Function |
Description |
|---|---|
createGiottoObject |
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createGiottoVisiumObject |
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createGiottoObjectSubcellular |
Giotto Helper Functions¶
Common functions to help working with Giotto objects
Function |
Description |
|---|---|
pDataDT |
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fDataDT |
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showProcessingSteps |
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calculateMetaTable |
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calculateMetaTableCells |
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combineMetadata |
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createMetagenes |
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findNetworkNeighbors |
Giotto Getters & Setters¶
Low level functions to get, set and show Giotto slots
Function |
Description |
|---|---|
get_expression_values |
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set_expression_values |
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get_spatial_locations |
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set_spatial_locations |
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get_dimReduction |
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set_dimReduction |
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get_NearestNetwork |
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set_NearestNetwork |
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get_spatialNetwork |
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set_spatialNetwork |
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get_spatialGrid |
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set_spatialGrid |
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get_polygon_info |
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set_polygon_info |
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get_feature_info |
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set_feature_info |
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get_spatial_enrichment |
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set_spatial_enrichment |
Giotto Show Slots¶
Show what is available in different information slots
Function |
Description |
|---|---|
showGiottoExpression |
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showGiottoSpatLocs |
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showGiottoDimRed |
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showGiottoSpatNetworks |
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showGiottoSpatGrids |
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showGiottoSpatialInfo |
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showGiottoFeatInfo |
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showGiottoSpatEnrichments |
Modify Giotto Object¶
Modifications to the Giotto objects
Function |
Description |
|---|---|
filterGiotto |
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subsetGiotto |
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subsetGiottoLocs |
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joinGiottoObjects |
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normalizeGiotto |
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adjustGiottoMatrix |
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annotateGiotto |
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removeCellAnnotation |
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removeFeatAnnotation |
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addCellMetadata |
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addFeatMetadata |
|
addFeatStatistics |
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addCellStatistics |
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addStatistics |
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addFeatsPerc |
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addCellIntMetadata |
Dimension Reduction¶
Functions to reduce dimensions.
Function |
Description |
|---|---|
calculateHVG |
|
signPCA |
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screePlot |
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jackstrawPlot |
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runPCA |
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runUMAP |
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runtSNE |
Clustering¶
Functions to cluster cells.
Function |
Description |
|---|---|
Create NN Network |
|
addNetworkLayout |
|
clusterCells |
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doLeidenCluster |
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doLouvainCluster |
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doKmeans |
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doHclust |
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subClusterCells |
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doLeidenSubCluster |
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doLouvainSubCluster |
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getClusterSimilarity |
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mergeClusters |
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getDendrogramSplits |
Marker Genes¶
Functions to detect cell type / cluster specific marker genes.
Function |
Description |
|---|---|
findMarkers |
|
findMarkers_one_vs_all |
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findGiniMarkers |
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findGiniMarkers_one_vs_all |
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findScranMarkers |
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findScranMarkers_one_vs_all |
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findMastMarkers |
|
findMastMarkers_one_vs_all |
Auxiliary Visualizations¶
Functions for different visualization options to explore gene, cell or cluster characteristics.
Function |
Description |
|---|---|
showClusterHeatmap |
|
showClusterDendrogram |
|
plotHeatmap |
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plotMetaDataHeatmap |
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plotMetaDataCellsHeatmap |
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violinPlot |
Spatial¶
Spatial Enrichment¶
Algorithms to compute spatial enrichment of gene signatures or scRNA-seq matrix
Function |
Description |
|---|---|
makeSignMatrixPAGE |
|
makeSignMatrixRank |
|
runSpatialEnrich |
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runPAGEEnrich |
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runRankEnrich |
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runHyperGeometricEnrich |
Spatial Deconvolution¶
Algorithms to perform spatial deconvolution based on gene signatures or single-cell RNAseq information
Function |
Description |
|---|---|
makeSignMatrixDWLSfromMatrix |
|
makeSignMatrixDWLS |
|
runSpatialDeconv |
|
runDWLSDeconv |
Spatial Network or Grid¶
Function to (help) create a spatial network or grid.
Function |
Description |
|---|---|
spatNetwDistributionsDistance |
|
spatNetwDistributionsKneighbors |
|
spatNetwDistributions |
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createSpatialDelaunayNetwork |
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plotStatDelaunayNetwork |
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createSpatialKNNnetwork |
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createSpatialNetwork |
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annotateSpatialNetwork |
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annotateSpatialGrid |
|
createSpatialGrid |
Spatial Expression Patterns¶
Methods to detect spatially coherent expression patterns.
Function |
Description |
|---|---|
binSpectSingleMatrix |
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binSpectMultiMatrix |
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binSpectSingle |
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binSpectMulti |
|
binSpect |
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spatialDE |
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spatialAEH |
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trendSceek |
|
spark |
Simulate Spatial Expression Patterns¶
Function to simulate a user-defined pattern using the full complexity of the different gene distributions.
Function |
Description |
|---|---|
simulateOneGenePatternGiottoObject |
|
runPatternSimulation |
Spatial Co-Expression Modules¶
Method to detect spatially co-expressed feature modules.
Function |
Description |
|---|---|
clusterSpatialCorGenes |
|
detectSpatialCorGenes |
|
heatmSpatialCorGenes |
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showSpatialCorGenes |
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rankSpatialCorGroups |
2D Visualization In Expression Space¶
Visualization of expression space (e.g. UMAP) in 2D.
Function |
Description |
|---|---|
dimPlot |
|
plotUMAP |
|
plotTSNE |
|
plotTSNE |
|
dimGenePlot |
|
dimCellPlot |
2D Visualization in Spatial Space¶
Visualization of expression space (e.g. UMAP) in 2D.
Function |
Description |
|---|---|
spatPlot |
|
spatCellPlot |
2D Visualization In Both Spatial And Expression Space¶
Visualization in both 2D spatial and expression space.
Function |
Description |
|---|---|
spatDimPlot |
|
spatDimCellPlot |
3D Visualization¶
3D Visualization Dimension Reduction¶
Visualization of expression space (e.g. UMAP) in 3D
Function |
Description |
|---|---|
dimPlot3D |
|
dimPlot3D |
|
plotTSNE_3D |
|
plotPCA_3D |
3D Visualization In Spatial Space¶
Visualization in 3D spatial space.
Function |
Description |
|---|---|
spatPlot3D |
3D visualization in Spatial and Expression Space¶
Visualization in 3D spatial space.
Function |
Description |
|---|---|
spatDimPlot3D |
In Silico Cross Sections¶
Functions to create an in silico 2D cross sections from 3D data.
Function |
Description |
|---|---|
createCrossSection |
|
crossSectionGenePlot |
|
crossSectionPlot |
|
crossSectionGenePlot3D |
|
crossSectionPlot3D |
|
insertCrossSectionSpatPlot3D |
|
insertCrossSectionGenePlot3D |
Cell Neighborhood¶
Cell Neighborhood: Cell-Type/Cell-Type Enrichment¶
Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.
Function |
Description |
|---|---|
cellProximityEnrichment |
|
cellProximityBarplot |
|
cellProximityHeatmap |
|
cellProximityNetwork |
|
cellProximitySpatPlot |
|
cellProximitySpatPlot3D |
Cell Neighborhood: Spatial Interaction Changed Genes (ICG)¶
Identify and visualize genes that change in a source cell type due to interaction with another neighboring cell type.
Function |
Description |
|---|---|
findInteractionChangedFeats |
|
findICF |
|
filterInteractionChangedFeats |
|
filterICF |
Cell Neighborhood: Ligand-Receptor Cell Communication¶
Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.
Function |
Description |
|---|---|
exprCellCellcom |
|
spatCellCellcom |
|
plotCCcomDotplot |
|
plotRankSpatvsExpr |
|
plotRecovery |
Interoperability¶
Convert other type of objects into a Giotto object.
Function |
Description |
|---|---|
seuratToGiotto |