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()

Assets 2

19 Apr 12:59

jiajic

v3.3.0

310ae37

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

Assets 2

18 Apr 21:55

jiajic

v3.2.0

2e3e46f

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