NEWS.md

Giotto 4.1.6 (2024/12/09)

Bug fixes

• doScrubletDetect() seed setting

Enhancements

• labelTransfer() now has integration_method = "harmony" for label transferring with an integration pipeline. See ?labelTransfer and the integration_method section.
• importXenium() load_transcripts() can now return a data.table rather than the giottoPoints representation

New

• doMesmerSegmentation() and doStardistSegmentation() segmentation wrappers
• .varexp() internal for calculating SVD variance determined with support for partial SVDs
• .cumvar() internal for calculating cumulative variance explained
• re-export of dotPlot() from GiottoVisuals

Changes

• GiottoClass req raised to 0.4.5
• GiottoUtils req raised to 0.2.2
• GiottoVisuals req raised to 0.2.10

Giotto 4.1.5 (2024/11/08)

Enhancements

• createGiottoXeniumObject() auto loading for morphology focus images, image directory loading, auto centroid calculation, allow skipping transcript loading

Website changes

• New Analysis mini tutorials for showing common processing functions independently of the spatial technology.
• New Slide-seq and OpenST examples.
• New Contributing tab with guidelines for contributing to the package and the website.
• New Visualizations tutorials.
• New Giotto workflow and Core Functions tutorials under Get Started tab.
• New Create and change Giotto instructions tutorial.
• New Spatial Patterns tutorials section.
• New tutorials under Interactivity for regions selection with vitessceR.
• New Multi-samples tutorials section.
• Updated technologies examples.
• Updated tutorials for using Docker and Singularity Giotto containers.
• Homogenized variable names across examples and tutorials.

Giotto 4.1.4 (2024/10/30)

Changes

• createGiottoVisiumObject() apply a modifier of 0.8461538 to visium spot diameter to reflect actual spot size
• doLeidenClusterIgraph() deprecate param resolution_parameter in favor of resolution

Enhancements

• createGiottoVisiumObject() append multiplicative scalefactor to get micron values from the current coordinate units during Visium object creation. Accessible through instructions(gobject, "micron_scale")

Giotto 4.1.3 (2024/10/27)

New

• Add giottoToAnndataZarr() to create a local anndata zarr folder and interact with the vitessceR package.
• reduceDims() API function for dimension reductions
• runNMF() implementation that works via RcppML

Changes

• runWNN() and runIntegratedUMAP() arguments were updated to make the function flexible to handle any number of modalities.
• update jackstrawPlot() to make more flexible and efficient. Changed default params for scaling, centering, and feats_to_use to match runPCA()
• change warning when reduction "feats" is selected in runtSNE() to error to avoid accidentally wiping the giotto object.

Giotto 4.1.2

Breaking changes

• remove deprecated PAGEEnrich(). Use runPAGEEnrich() instead
• remove deprecated rankEnrich(). Use runRankEnrich() instead
• remove deprecated hyperGeometricEnrich(). Use runHyperGeometricEnrich() instead
• remove deprecated createSpatialEnrich(). Use runSpatialEnrich() instead
• remove deprecated heatmSpatialCorGenes(). Use heatmSpatialCorFeats() instead
• remove deprecated runPAGEEnrich_OLD(). Use runPAGEEnrich() instead
• remove do_pca, expression_values, feats_to_use args from runGiottoHarmony(). Running PCA during the harmony::RunHarmony() call is deprecated.

Enhancements

• add 'quantile' normalization method to normalizeGiotto()

Changes

• limma, plotly, and Rtsne moved to Suggests
• move progressr and jsonlite dependencies to GiottoUtils v0.1.12
• remove reshape2 dependency.

Bug fixes

• processGiotto() can now skip adjust step by default

New

• identifyTMAcores() for assigning IDs to tissue microarray spatial data.
• labelTransfer() for transferring labels between giotto objects or subsets thereof. Supercedes doClusterProjection()

Giotto 4.1.1

Bug fixes

• Allow giottoInstructions passing for Xenium convenience functions

Changes

• Deprecate screePlot() name in favor of dim_reduction_name param

Giotto 4.1.0 (2024/07/31)

Breaking changes

• Deprecated detectSpatialCorGenes() removed. Use detectSpatialCorFeats() instead
• Deprecated findInteractionChangedGenes() removed. Use findInteractionChangedFeats() instead
• Deprecated findCellProximityGenes() removed. Use findInteractionChangedFeats() instead
• createGiottoXeniumObject() has been overhauled and parameters have changed.

Bug fixes

• Fix error in plotInteractivePolygons() when providing a spatial plot with a continuous scale #964 by jweis3
• Fix error in DWLS find_dampening_constant() when S[subset, ] produces only 1 gene.
• Fix error in interpolateFeatures() where feature names with - or starting with numbers did not work
• Add catch in runPCAprojectionBatch() for when ncp requested exceeds number of feats used
• Make spatCellCellcom() respect verbose flag #949 by rbutleriii

New

• Dataset affine registration via interactive shiny app and automated SIFT detection
• Cell segmentation via Cellpose
• read10xAffineImage() for reading 10x affine transformed images
• Several modular importer and convenience functions
• ONTraC implementation

Enhancements

• print() methods for icfObject and combIcfObject

Changes

• require GiottoUtils (>= 0.1.10)
• require GiottoClass (>= 0.3.3)

Giotto 4.0.8 (2024/05/22)

Breaking changes

• crossSectionGenePlot() removed. Use crossSectionFeatPlot() instead
• crossSectionGenePlot3D() removed. Use crossSectionFeatPlot3D() instead
• insertCrossSectionGenePlot3D() removed Use insertCrossSectionFeatPlot3D() instead

Bug fixes

• binSpect() param passing error introduced in v4.0.6
• updated viewHMRFresults3D() and viewHMRFresults2D()
• updated createCrossSections(), insertCrossSectionSpatPlot3D(), crossSectionPlot(), crossSectionFeatPlot3D(), insertCrossSectionFeatPlot3D(), crossSectionPlot3D(), crossSectionFeatPlot()

Changes

• GiottoVisuals (>= 0.2.2), GiottoClass (>= 0.3.1), GiottoUtils (>= 0.1.8) are now required.

Giotto 4.0.6 (2024/05/13)

Enhancements

• New interpolateFeature() for kriging interpolation of values

Changes

• GiottoVisuals (>= 0.2.0) and GiottoClass (>= 0.3.0) are now required.

Giotto 4.0.5 (2024/03/12)

Bug fixes

• Fix Error "cannot coerce class ‘structure("spatLocsObj", package = "Giotto")’ to a data.frame" in spatialDE()

Enhancements

• readPolygonVizgenParquet() now has calc_centroids = TRUE by default

Giotto 4.0.4 (2024/02/28)

Breaking changes

• Remove do_manual_adj and image adjustment params from createGiottoVisiumObject()
• createGiottoVisiumObject() now creates giottoLargeImage for spatial images.
• exprCellCellcom() deprecated gene_set_* params removed

Bug fixes

• Fix metadata appending/sorting issues introduced by GiottoClass v0.1.3 (2024/01/12). Affected functions: addHMRF(), addFeatsPerc(), doScrubletDetect()
• findNetworkNeighbors() now has default spatial_network_name value of NULL
• get10Xmatrix() now obeys split_by_type = FALSE

Changes

• Deprecate set.seed in favor of seed param for binSpect()
• binSpect() now sets a seed by default for reproducibility
• pkgdown files moved to separate repo

Enhancements

• Use mixedsort() for unique clusters metadata info
• Remove unnecessary matrix densification and expose seed param in doScrubletDetect()
• Remove unnecessary matrix densification in makeSignMatrixRank()

Giotto 4.0.3 (2024/02/20)

Bug fixes

• Remove old argument type_default = list(pal = c('blue', 'yellow', 'red')) in plotRankSpatvsExpr()

Giotto 4.0.2 (2023/12/21)

Bug Fixes

• fix bug in doHclust()

Changes

• Move GiottoClass back to depends to fix access to some generics

Giotto 4.0.1 (2023/12/16)

Breaking changes

• Remove cell_ids param for calculateHVF() in favor of simpler random_subset
• Move GiottoUtils, GiottoClass, and GiottoVisuals to imports

Added

• Add parse_affine() for interpreting affine transform matrices
• Add seed setting to runGiottoHarmony()
• Add parallelized calculation for calculateHVF() when a future plan is set

Changes

• Fix createGiottoXeniumObject() feature metadata reading for .json file
• Update runGiottoHarmony() to call harmony::RunHarmony()
• Update Matrix requirement to >= 1.6.2 (a re-install of irlba may resolve issues with Matrix incompatibility.)

Giotto 4.0.0 (2023/11/29)

Breaking changes

• Update to modular package organization with the main packages being GiottoUtils, GiottoClass, GiottoVisuals, and Giotto as the analytical umbrella package.

Added

• New File spatial_enrichment_visuals.R
• New function findCellTypesFromEnrichment() within spatial_enrichment_visuals.R to show most probable cell types based on a provided enrichment
• New function plotCellTypesFromEnrichment() within spatial_enrichment_visuals.R that generates a bar plot of cell types vs frequency based on a provided enrichment
• New function pieCellTypesFromEnrichment() within spatial_enrichment_visuals.R that generates a pie chart of cell types based on a provided enrichment
• New function addVisiumPolygons() within convenience.R (along with its requisite internal functions) that adds circular polygons centered at the spatial locations of a Giotto Object made with Visium data. Takes a Giotto Object and a path to the Visium output file scalefactors_json.json as input arguments.
• Added addVisiumPolygons() to createGiottoVisiumObject() workflow.
• Add cell_ids param to calculateHVF() to allow calculation of HVFs on a subset of cells
• Add seed setting to runGiottoHarmony()
• Update runGiottoHarmony() to call harmony::RunHarmony()

Changes

• Update Matrix requirement to >= 1.6.3

Giotto 3.3.1 (2023/08/02)

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()

Giotto 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 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 overallocation for data.tablesbased objects after loading from disk

Giotto 3.1.0 (2022/12/01)

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 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 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 2.1.0 (2022/11/09)

Breaking changes

• Update of python version to 3.10.2 details

Added

• New anndataToGiotto() to convert scanpy anndata to Giotto

Giotto 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