NEWS.md
doScrubletDetect() seed settinglabelTransfer() 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 representationdoMesmerSegmentation() and doStardistSegmentation() segmentation wrappers.varexp() internal for calculating SVD variance determined with support for partial SVDs.cumvar() internal for calculating cumulative variance explaineddotPlot() from GiottoVisualscreateGiottoXeniumObject() auto loading for morphology focus images, image directory loading, auto centroid calculation, allow skipping transcript loadingcreateGiottoVisiumObject() apply a modifier of 0.8461538 to visium spot diameter to reflect actual spot sizedoLeidenClusterIgraph() deprecate param resolution_parameter in favor of resolution
createGiottoVisiumObject() append multiplicative scalefactor to get micron values from the current coordinate units during Visium object creation. Accessible through instructions(gobject, "micron_scale")
giottoToAnndataZarr() to create a local anndata zarr folder and interact with the vitessceR package.reduceDims() API function for dimension reductionsrunNMF() implementation that works via RcppMLrunWNN() and runIntegratedUMAP() arguments were updated to make the function flexible to handle any number of modalities.jackstrawPlot() to make more flexible and efficient. Changed default params for scaling, centering, and feats_to_use to match runPCA()
runtSNE() to error to avoid accidentally wiping the giotto object.PAGEEnrich(). Use runPAGEEnrich() insteadrankEnrich(). Use runRankEnrich() insteadhyperGeometricEnrich(). Use runHyperGeometricEnrich() insteadcreateSpatialEnrich(). Use runSpatialEnrich() insteadheatmSpatialCorGenes(). Use heatmSpatialCorFeats() insteadrunPAGEEnrich_OLD(). Use runPAGEEnrich() insteaddo_pca, expression_values, feats_to_use args from runGiottoHarmony(). Running PCA during the harmony::RunHarmony() call is deprecated.'quantile' normalization method to normalizeGiotto()
limma, plotly, and Rtsne moved to Suggestsprogressr and jsonlite dependencies to GiottoUtils v0.1.12reshape2 dependency.processGiotto() can now skip adjust step by defaultidentifyTMAcores() for assigning IDs to tissue microarray spatial data.labelTransfer() for transferring labels between giotto objects or subsets thereof. Supercedes doClusterProjection()
screePlot() name in favor of dim_reduction_name paramdetectSpatialCorGenes() removed. Use detectSpatialCorFeats() insteadfindInteractionChangedGenes() removed. Use findInteractionChangedFeats() insteadfindCellProximityGenes() removed. Use findInteractionChangedFeats() insteadcreateGiottoXeniumObject() has been overhauled and parameters have changed.plotInteractivePolygons() when providing a spatial plot with a continuous scale #964 by jweis3find_dampening_constant() when S[subset, ] produces only 1 gene.interpolateFeatures() where feature names with - or starting with numbers did not workrunPCAprojectionBatch() for when ncp requested exceeds number of feats usedspatCellCellcom() respect verbose flag #949 by rbutleriiiread10xAffineImage() for reading 10x affine transformed imagesprint() methods for icfObject and combIcfObject
crossSectionGenePlot() removed. Use crossSectionFeatPlot() insteadcrossSectionGenePlot3D() removed. Use crossSectionFeatPlot3D() insteadinsertCrossSectionGenePlot3D() removed Use insertCrossSectionFeatPlot3D() insteadbinSpect() param passing error introduced in v4.0.6
viewHMRFresults3D() and viewHMRFresults2D()
createCrossSections(), insertCrossSectionSpatPlot3D(), crossSectionPlot(), crossSectionFeatPlot3D(), insertCrossSectionFeatPlot3D(), crossSectionPlot3D(), crossSectionFeatPlot()
interpolateFeature() for kriging interpolation of valuesspatialDE()
readPolygonVizgenParquet() now has calc_centroids = TRUE by defaultdo_manual_adj and image adjustment params from createGiottoVisiumObject()
createGiottoVisiumObject() now creates giottoLargeImage for spatial images.exprCellCellcom() deprecated gene_set_* params removedaddHMRF(), addFeatsPerc(), doScrubletDetect()
findNetworkNeighbors() now has default spatial_network_name value of NULL
get10Xmatrix() now obeys split_by_type = FALSE
set.seed in favor of seed param for binSpect()
binSpect() now sets a seed by default for reproducibilitymixedsort() for unique clusters metadata infoseed param in doScrubletDetect()
makeSignMatrixRank()
doHclust()
cell_ids param for calculateHVF() in favor of simpler random_subset
parse_affine() for interpreting affine transform matricesrunGiottoHarmony()
calculateHVF() when a future plan is setcreateGiottoXeniumObject() feature metadata reading for .json filerunGiottoHarmony() to call harmony::RunHarmony()
GiottoUtils, GiottoClass, GiottoVisuals, and Giotto as the analytical umbrella package.spatial_enrichment_visuals.R
findCellTypesFromEnrichment() within spatial_enrichment_visuals.R to show most probable cell types based on a provided enrichmentplotCellTypesFromEnrichment() within spatial_enrichment_visuals.R that generates a bar plot of cell types vs frequency based on a provided enrichmentpieCellTypesFromEnrichment() within spatial_enrichment_visuals.R that generates a pie chart of cell types based on a provided enrichmentaddVisiumPolygons() 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.addVisiumPolygons() to createGiottoVisiumObject() workflow.cell_ids param to calculateHVF() to allow calculation of HVFs on a subset of cellsrunGiottoHarmony()
runGiottoHarmony() to call harmony::RunHarmony()
checkGiottoEnvironment(). Downgrade from error to message and return FALSE when a provided directory does not existpoly_influence.R
showPolygonSizeInfluence() within poly_influence.R to show if cells switch clusters when across resized polygon annotationsshowCellProportionSwitchedPie() within poly_influence.R to visualize results from showPolygonSizeInfluence() in a pie chartshowCellProportionSwitchedSankey() within poly_influence.R to visualize results from showPolygonSizeInfluence() in a Sankey diagrammakePseudoVisium() within giotto_structure.R to generate a pseudo visium grid of circular spotstessellate() within giotto_structure.R to generate a grid of hexagons or squares for spatial binningfeature_set_enrichment.R
doFeatureSetEnrichment() within feature_set_enrichment.R for GSEA analysisdoGiottoClustree() within clustering.R for visualizations of leiden clusters at varying resolutionscreateArchRProj() and CreateGiottoObjectFromArchR() functions to create a giotto object with ATAC or epigenetic features using the ArchR pipeline.giottoMasterToSuite() function to convert a giotto object created with the master version to a Giotto suite object.readPolygonVizgenParquet() for updated parquet outputscreate function for exprObj creationspatial_manipulation.R
ext() methods for giottoPolygon, giottoPoints, spatialNetworkObj, spatLocsObj, giottoLargeImage
flip() methods for giottoPolygon, giottoPoints, spatialNetworkObj, spatLocsObj, SpatExtent, giottoLargeImage
giottoLargeImage plot() method.combine_matrices()
createGiottoObject() that will not allow object creation without supplied expression informationpolyStamp() to replace an apply function with a crossjoin for better performance.spatInSituPlotPoints() with plot_last parameter. Default output now plots polygons above points for better visibility.readPolygonFilesVizgenHDF5() add option to return as data.table and skip giottoPolygon creation. Downstream giottoPolygon creation refactored as new internal functioncreateGiottoVisiumObject() image h5 scalefactors reading to use partial matching for whether hi or lowres image is suppliedgiottoLargeImage plot() method to use terra::plot() instead of terra::plotRGB() for grayscale imagessubsetGiotto()
readCellMetadata() and readFeatMetadata()
accessors.R
set_default_feat_type() error downgraded to warning when no feat_types exist for given spat_unit
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 optionscreate_dimObject() internal function. Keeping create_dim_obj()
anndataToGiotto() and giottoToAnnData() for Nearest Neighbor and Spatial Networkscheck_py_for_scanpy() function, shifting code around in anndataToGiotto()
initialize() method for giotto
create constructor functions for Giotto S4 subobjectsactiveSpatUnit() and activeFeatType() for getting and setting active defaults on gobjectget_*_list() internal functions for retrieving list of all objects of a particular class for a spat_unit and feat_typeinstructions() generic for giotto to access and edit giottoInstructions
centroids() method for giottoPolygon to get centroid infooverlaps() generic for accessing overlaps slot of giottoPolygon
[ and [<* (empty) access generics to get the data from main slots of giottoPolygon and giottoPoints
getOption('giotto.cores'))giottoPoints from getFeatureInfo (default is still SpatVector)spatVector_to_dt2 internal as a barebones alternative to spatVector_to_dt()
getRainbowColors() color paletteassign_objnames_2_list() and assign_listnames_2_obj() internals for passing list names to object @name slots and vice versatest_createObject.R script for read functions/S4 subobject creationtest_accessors.R script for accessor functionstest_gobject.R script for gobject consistency checksinstallGiottoEnvironment() and downstream internal functions to allow custom python installation with a new argument, mini_install_path.checkGiottoEnvironment() to account for custom python installations with a new argument, mini_install_path.removeGiottoEnvironment() to account for custom python installations with a new argument, mini_path.createGiottoObject() with new data ingestion pipelinecell_ID, feat_ID, cell_metadata, feat_metadata slot initializationread_expression_data() and evaluate_expr_matrix() to be compatible with exprObj
changeGiottoInstructions() to allow addition of new params and enforce logical class of known paramscreateGiottoCosMxObject() associated with polygon placement and generationplot() for giottoPoints with faster rasterized plotting option. (Now used by default)doLouvainCluster() (sub)functions and made them compatible with new Giotto Suite framework.gefToGiotto() bin_size arguments.loadGiotto() and saveGiotto() with path.expand to expand provided file/directory pathscheck functions in giotto.R for checking gobject consistency during initialize()
evaluate functions in data_evaluation.R for data wrangling of external dataread functions in data_input.R for ingesting data and converting to list of Giotto native S4 subobjectsdd.R for inheriting commonly used documentationcreate_featureNetwork_object(), create_giotto_points_object(), create_giotto_polygon_object() to classes.Rdepth() from giotto.R to utilities.R@nn_network slotcreateSpatialNetwork() 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'
createGiottoCosMxObject() aggregate and all workflows until they are updatedgefToGiotto() interoperability function to convert gef object from Stereo*seq to giottogiottoToAnnData() interoperability function to convert giotto object to squidpy flavor anndata .h5ad file(s)giottoToSpatialExperiment() and spatialExperimentToGiotto() to convert between Giotto and SpatialExperimentspatialAutoCorLocal() and spatialAutoCorGlobal() functions to find spatial autocorrelations from expression and cell metadata informationcreateSpatialWeightMatrix() function to generate spatial weight matrix from spatial networks for autocorrelationmultiomics slot in giotto
coord_fix_ratio param to spatFeatPlot2D() and spatFeatPlot2D_single()
order parameter to dimFeatPlot2D and spatDimFeatPlot2d to plot and order cells according to the levels of the selected feature (#477)plot() method for spatialNetworkObj
set_row_order_dt() internal for setting data.table to a specific row order by referencefread_colmatch() internal for fread loading a subset of rows based on matches in a specified columncreate_nn_net_obj() internal constructor function for S4 nnNetObj
id_col, x_col, y_col params to polyStamp() to make stamp location input more flexibleoptional and custom_msg params to package_check()
wrap() and vect() generics for giotto, giottoPoints, and giottoPolygons
rotate(), t(), and spatShift generics for giotto subobject spatial manipulationspatIDs() and featIDs() genericsobjName() and objName generics for setting the names of relevant S4 subobjectsrbind() generic to append giottoPolygon objectsexactextractr and sf to “suggests” packagesprogressr to “imports” packagesgiotto.R to convenience.R
addFeatMetadata() to handle replacement of existing columnsshow() method for giotto
show() method for spatEnrObj
polygon_feat_names param in favor of z_indices in readPolygonFilesVizgenHDF5()
xy_translate_spatial_locations() in favor of shift_spatial_locations()
readPolygonFilesVizgen()
replaceGiottoInstructions() where instructions with more slots than previous are not allowedloadGiotto() that prevents proper parsing of filenames when spat_unit or feat_type contains ’_’ charactersloadGiotto() loss of overallocation for data.tablesbased objects after loading from diskinitialize() generic that calls setalloccol() for data.table*based S4 subobjects to allow setting by referencespatUnit, spatUnit<*, featType, and featType<* feat type generics for S4 subobjects for setting the relevant slotshexVertices() to polygon shape array generation functionalitycreateGiottoCosMxObject() for 3.0 and modularization of functions. ‘subcellular’ workflow has been tested to work along with an updated tutorial.cow_n_col paramannotateGiotto() after 3.0 update (#433)joinGiottoObjects() metadata processingshow functions with options("giotto.color_show" = FALSE)
extract_polygon_list() (#433)show functions for Latin1 systemscreateGiottoXeniumObject() for loading 10x Xenium data[] and []<* to get or set information into the main data slot@provenance slot in S4 subobjects to track provenance of aggregated information (z_layers used for example)calculateOverlapPolygonImages() for calculating overlapped intensities from image*based information (e.g. IMC, IF, MIBI, …) and polygon data (e.g. cell)overlapImagesToMatrix() converts intensity*polygon overlap info into an expression matrix (e.g. cell by protein)aggregateStacks() set of functions work with multiple subcellular layers when generating aggregated expression matricesanndataToGiotto() to convert scanpy anndata to GiottoGiottoData package to work with spatial datasets associated with Giotto
getSpatialDataset() and loadGiottoMini() functions to this packagesaveGiotto() and loadGiotto() for preserving memory*pointer based objects. In general_help.R
saveRDS() that also works with spatVector and spatRaster pointers.plotInteractivePolygon() for plot*interactive polygonal selection of points.polyStamp(), circleVertices, rectVertices. In giotto_structures.R
get_CellMetadata (alias of pDataDT()), set_CellMetadata, get_FeatMetadata (alias of fDataDT()), set_FeatMetadata. See accessors.R
filterDistributions() to generate histogram plots from expression statisticsplotInteractionChangedGenes() ,plotICG(), plotCPG() in favor of plotInteractionChangedFeatures() and plotICF() and plotCPF()
plotCellProximityGenes(), in favor of plotCellProximityFeatures()
plotCombineInteractionChangedGenes(), plotCombineICG(), plotCombineCPG() in favor of plotCombineInteractionChangedFeatures() and plotCombineICF()
findInteractionChangedGenes(), findICG(), findCPG() in favor of findInteractionChangedFeats() and findICF
filterInteractionChangedGenes(), filterICG(), filterCPG() in favor of filterInteractionChangedFeats() and filterICF()
combineInteractionChangedGenes(), combineICG(), combineCPG() in favor of combineInteractionChangedFeats() and combineICF()
combineCellProximityGenes_per_interaction() in favor of combineCellProximityFeatures_per_interaction()