v3.3.1

Breaking Changes

• Change checkGiottoEnvironment(). Downgrade from error to message and return FALSE when a provided directory does not exist

Added

• New file poly_influence.R
• New function showPolygonSizeInfluence() within poly_influence.R to show if cells switch clusters when across resized polygon annotations
• New function showCellProportionSwitchedPie() within poly_influence.R to visualize results from showPolygonSizeInfluence() in a pie chart
• New function showCellProportionSwitchedSankey() within poly_influence.R to visualize results from showPolygonSizeInfluence() in a Sankey diagram
• New function makePseudoVisium() within giotto_structure.R to generate a pseudo visium grid of circular spots
• New function tessellate() within giotto_structure.R to generate a grid of hexagons or squares for spatial binning
• New file feature_set_enrichment.R
• New function doFeatureSetEnrichment() within feature_set_enrichment.R for GSEA analysis
• New function doGiottoClustree() within clustering.R for visualizations of leiden clusters at varying resolutions
• New createArchRProj() and CreateGiottoObjectFromArchR() functions to create a giotto object with ATAC or epigenetic features using the ArchR pipeline.
• New giottoMasterToSuite() function to convert a giotto object created with the master version to a Giotto suite object.
• New readPolygonVizgenParquet() for updated parquet outputs
• Add checkmate to Imports for assertions checking
• Add exported create function for exprObj creation
• New file spatial_manipulation.R
• Add ext() methods for giottoPolygon, giottoPoints, spatialNetworkObj, spatLocsObj, giottoLargeImage
• Add flip() methods for giottoPolygon, giottoPoints, spatialNetworkObj, spatLocsObj, SpatExtent, giottoLargeImage
• Add access to terra plotting params for giottoLargeImage plot() method.

Changes

• Fix bug in combine_matrices()
• Fix bug in createGiottoObject() that will not allow object creation without supplied expression information
• Updated polyStamp() to replace an apply function with a crossjoin for better performance.
• Updated spatInSituPlotPoints() with plot_last parameter. Default output now plots polygons above points for better visibility.
• Add check for spatLocsObj for spatlocs in polyStamp()
• Removed various print() and cat() statements throughout.
• Changed default verbose argument to FALSE for createGiottoObject
• Changed default verbose argument to FALSE for joinGiottoObjects
• Changed default verbose argument to FALSE for createGiottoObjectSubcellular
• Default verbose = FALSE argument added to cellProximityEnrichmentSpots
• Default verbose = FALSE argument added to specific_CCCScores_spots
• Default verbose = FALSE argument added to runWNN
• Default verbose = FALSE argument added to subset_giotto_points_object
• Default verbose = FALSE argument added to subset_feature_info_data
• Default verbose = FALSE argument added to subsetGiotto
• Default verbose = FALSE argument added to subsetGiottoLocsSubcellular
• Default verbose = FALSE argument added to createGiottoXeniumObject_subcellular
• Update readPolygonFilesVizgenHDF5() add option to return as data.table and skip giottoPolygon creation. Downstream giottoPolygon creation refactored as new internal function
• Update cell segmentation workflow to check for deepcell and PIL python packages
• Update cell segmentation workflow to return grayscale mask images instead of RGB
• Update createGiottoVisiumObject() image h5 scalefactors reading to use partial matching for whether hi or lowres image is supplied
• Update giottoLargeImage plot() method to use terra::plot() instead of terra::plotRGB() for grayscale images
• Remove unnecessary prints from subsetGiotto()
• Fix bug in readCellMetadata() and readFeatMetadata()