v3.3.0

Breaking Changes

• Removed all deprecated accessors from accessors.R
• set_default_feat_type() error downgraded to warning when no feat_types exist for given spat_unit
• update loadGiotto() and saveGiotto() to allow using long strings as column names in the spatVector objects
• 'active_spat_unit' and 'active_feat_type' params that can be set through instructions() are now used instead of 'giotto.spat_unit' and 'giotto.feat_type' global options
• removed duplicate create_dimObject() internal function. Keeping create_dim_obj()

Added

• New implementations of anndataToGiotto() and giottoToAnnData() for Nearest Neighbor and Spatial Networks
• New check_py_for_scanpy() function, shifting code around in anndataToGiotto()
• Add initialize() method for giotto
• Add exported create constructor functions for Giotto S4 subobjects
• Add activeSpatUnit() and activeFeatType() for getting and setting active defaults on gobject
• New get_*_list() internal functions for retrieving list of all objects of a particular class for a spat_unit and feat_type
• Add instructions() generic for giotto to access and edit giottoInstructions
• Add centroids() method for giottoPolygon to get centroid info
• Add overlaps() generic for accessing overlaps slot of giottoPolygon
• Add [ and [<- (empty) access generics to get the data from main slots of giottoPolygon and giottoPoints
• Add cores detection to run on package attach. (getOption('giotto.cores'))
• Add option to return as giottoPoints from getFeatureInfo (default is still SpatVector)
• Add spatVector_to_dt2 internal as a barebones alternative to spatVector_to_dt()
• Add getRainbowColors() color palette
• New assign_objnames_2_list() and assign_listnames_2_obj() internals for passing list names to object @name slots and vice versa
• New test_that test_createObject.R script for read functions/S4 subobject creation
• New test_that test_accessors.R script for accessor functions
• New test_that test_gobject.R script for gobject consistency checks

Changes

• Update installGiottoEnvironment() and downstream internal functions to allow custom python installation with a new argument, mini_install_path.
• Update checkGiottoEnvironment() to account for custom python installations with a new argument, mini_install_path.
• Update removeGiottoEnvironment() to account for custom python installations with a new argument, mini_path.
• Update createGiottoObject() with new data ingestion pipeline
• Modify cell_ID, feat_ID, cell_metadata, feat_metadata slot initialization
• Update read_expression_data() and evaluate_expr_matrix() to be compatible with exprObj
• Change changeGiottoInstructions() to allow addition of new params and enforce logical class of known params
• Update and fix bugs in createGiottoCosMxObject() associated with polygon placement and generation
• Update plot() for giottoPoints with faster rasterized plotting option. (Now used by default)
• Fix bug in doLouvainCluster() (sub)functions and made them compatible with new Giotto Suite framework.
• Fix bug in gefToGiotto() bin_size arguments.
• Update loadGiotto() and saveGiotto() with path.expand to expand provided file/directory paths
• Organize new and refactored slot check functions in giotto.R for checking gobject consistency during initialize()
• Organize new and refactored evaluate functions in data_evaluation.R for data wrangling of external data
• Organize new and refactored read functions in data_input.R for ingesting data and converting to list of Giotto native S4 subobjects
• Organize dummy documentation in dd.R for inheriting commonly used documentation
• Moved create_featureNetwork_object(), create_giotto_points_object(), create_giotto_polygon_object() to classes.R
• Moved depth() from giotto.R to utilities.R