NEWS.md

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Giotto Suite 3.3.0 (2023-04-18)

Breaking Changes

• Set Suite as default branch
• 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

Giotto Suite 3.2.0 (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
• Removed createGiottoCosMxObject() aggregate and all workflows until they 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

Giotto Suite 3.1.0 (2202-12-01)

Added

• New initialize() generic that calls setalloccol() for data.table-based S4 subobjects to allow setting by reference
• New spatUnit, spatUnit<-, featType, and featType<- feat type generics for S4 subobjects for setting the relevant slots
• Add hexVertices() to polygon shape array generation functionality

Changes

• Update createGiottoCosMxObject() for 3.0 and modularization of functions. 'subcellular' workflow has been tested to work along with an updated tutorial.
• Update grid plotting behavior to set a default number columns to use based on number of elements to plot. Can be overridden by explicitly providing input to cow_n_col param
• Fix bug in annotateGiotto() after 3.0 update (#433)
• Fix bug in joinGiottoObjects() metadata processing
• Update seed setting behavior in dimension_reduction.R and clustering.R

Giotto Suite 3.0.1 (2022-11-20)

Added

• New system color support detection (based on crayon package logic)
• Add ability to turn off colored text in show functions with options("giotto.color_show" = FALSE)

Changes

• Fix bug in extract_polygon_list() (#433)
• Update Unicode character printing with show functions for Latin1 systems

Giotto Suite 3.0.0 (2022-11-18)

Breaking Changes

• S4 subobjects framework will require giotto objects to be remade

Added

• New createGiottoXeniumObject() for loading 10x Xenium data
• New S4 subobjects. Details can be found in classes.R
• New basic generics for S4 subobjects. Mainly the use of [] and []<- to get or set information into the main data slot
• New @provenance slot in S4 subobjects to track provenance of aggregated information (z_layers used for example)
• New calculateOverlapPolygonImages() for calculating overlapped intensities from image-based information (e.g. IMC, IF, MIBI, ...) and polygon data (e.g. cell)
• New overlapImagesToMatrix() converts intensity-polygon overlap info into an expression matrix (e.g. cell by protein)
• New aggregateStacks() set of functions work with multiple subcellular layers when generating aggregated expression matrices

Changes

• Update setter functions to read the @spat_unit and @feat_type slots of subobjects to determine nesting
• Update of show functions to display color coded nesting names and tree structure

Giotto Suite 2.1.0 (2202-11-09)

Breaking Changes

• Update of python version to 3.10.2 details

Added

• New anndataToGiotto() to convert scanpy anndata to Giotto

Giotto Suite 2.0.0.998

Added

• New GiottoData package to work with spatial datasets associated with Giotto
  • Stores the minidatasets: preprocessed giotto objects that are ready to be used in any function
  • Moved: getSpatialDataset() and loadGiottoMini() functions to this package
• New saveGiotto() and loadGiotto() for preserving memory-pointer based objects. In general_help.R
• It saves a Giotto object into a folder using a specific structure. Essentially a wrapper around saveRDS() that also works with spatVector and spatRaster pointers.
• New plotInteractivePolygon() for plot-interactive polygonal selection of points.
• New polygon shape array creation through polyStamp(), circleVertices, rectVertices. In giotto_structures.R
• Add accessor functions get_CellMetadata (alias of pDataDT()), set_CellMetadata, get_FeatMetadata (alias of fDataDT()), set_FeatMetadata. See accessors.R
• New filterDistributions() to generate histogram plots from expression statistics

Changes

• Deprecate plotInteractionChangedGenes() ,plotICG(), plotCPG() in favor of plotInteractionChangedFeatures() and plotICF() and plotCPF()
• Deprecate plotCellProximityGenes(), in favor of plotCellProximityFeatures()
• Deprecate plotCombineInteractionChangedGenes(), plotCombineICG(), plotCombineCPG() in favor of plotCombineInteractionChangedFeatures() and plotCombineICF()
• Deprecate findInteractionChangedGenes(), findICG(), findCPG() in favor of findInteractionChangedFeats() and findICF
• Deprecate filterInteractionChangedGenes(), filterICG(), filterCPG() in favor of filterInteractionChangedFeats() and filterICF()
• Deprecate combineInteractionChangedGenes(), combineICG(), combineCPG() in favor of combineInteractionChangedFeats() and combineICF()
• Deprecate combineCellProximityGenes_per_interaction() in favor of combineCellProximityFeatures_per_interaction()

Breaking Changes

• ICF output internal object structure names have changed to use feats instead of genes

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.