Giotto is now a modularized suite of packages.
This version is paired with our bioRxiv pre-print

Final Giotto version prior to 4.0.0 modularization.

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()

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

(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

Release of Giotto Suite branch.

This is the first release after merging the development branch with master following the 'ours' strategy as detailed in https://stackoverflow.com/questions/2862590/how-to-replace-master-branch-in-git-entirely-from-another-branch

The previous master branch is copied to a new branch called 'old_master'.

Last release of original master branch. This branch will be re-named old_master. Development and master will be merged.

Release version with reduced dependencies and hf5 option for visium data

Full update on Giotto.
See https://rubd.github.io/Giotto_site/news/index.html#giotto-1-0-0 for more details.