v3.2.0

(Originally Released 2023-02-02)

Breaking Changes

• Removed support for deprecated nesting in @nn_network slot
• createSpatialNetwork() will now output a spatialNetworkObj by default when return_gobject = FALSE. It is possible to change this back to the data.table output by setting output = 'data.table'
• Set incomplete classes in classes.R as virtual to prevent their instantiation
• Only createGiottoCosMxObject() subcellular workflow available until the others are updated

Added

• New gefToGiotto() interoperability function to convert gef object from Stereo-seq to giotto
• New giottoToAnnData() interoperability function to convert giotto object to squidpy flavor anndata .h5ad file(s)
• New giottoToSpatialExperiment() and spatialExperimentToGiotto() to convert between Giotto and SpatialExperiment
• New spatialAutoCorLocal() and spatialAutoCorGlobal() functions to find spatial autocorrelations from expression and cell metadata information
• New createSpatialWeightMatrix() function to generate spatial weight matrix from spatial networks for autocorrelation
• Add spatial_interaction_spot.R with functions adapted from master branch for working with the Giotto suite object.
• New exported accessors for slots (experimental)
• New multiomics slot in giotto
• Add coord_fix_ratio param to spatFeatPlot2D() and spatFeatPlot2D_single()
• Add order parameter to dimFeatPlot2D and spatDimFeatPlot2d to plot and order cells according to the levels of the selected feature (#477)
• Add plot() method for spatialNetworkObj
• New set_row_order_dt() internal for setting data.table to a specific row order by reference
• New fread_colmatch() internal for fread loading a subset of rows based on matches in a specified column
• Add missing create_nn_net_obj() internal constructor function for S4 nnNetObj
• Add id_col, x_col, y_col params to polyStamp() to make stamp location input more flexible
• Add optional and custom_msg params to package_check()
• New wrap() and vect() generics for giotto, giottoPoints, and giottoPolygons
• New rotate(), t(), and spatShift generics for giotto subobject spatial manipulation
• New spatIDs() and featIDs() generics
• New objName() and objName generics for setting the names of relevant S4 subobjects
• New rbind() generic to append giottoPolygon objects
• Add packages exactextractr and sf to "suggests" packages
• Add package progressr to "imports" packages

Changes

• Move giotto object method-specific creation functions from giotto.R to convenience.R
• Update addFeatMetadata() to handle replacement of existing columns
• Update show() method for giotto
• Update show() method for spatEnrObj
• Deprecate older snake_case accessors
• Deprecate polygon_feat_names param in favor of z_indices in readPolygonFilesVizgenHDF5()
• Deprecate xy_translate_spatial_locations() in favor of shift_spatial_locations()
• Optimize readPolygonFilesVizgen()
• Fix bug in replaceGiottoInstructions() where instructions with more slots than previous are not allowed
• Fix bug in loadGiotto() that prevents proper parsing of filenames when spat_unit or feat_type contains '_' characters
• Fix loadGiotto() loss of over-allocation for data.tables-based objects after loading from disk