Man pages for drieslab/Giotto_site_suite
Spatial Single-Cell Transcriptomics Toolbox
| abb_mat | Print abbreviated matrix |
| abb_spatlocs | Print abbreviated spatlocs |
| activeFeatType-generic | Active feature type |
| activeSpatUnit-generic | Active spatial unit |
| adapt_aspect_ratio | adapt_aspect_ratio |
| addCellIntMetadata | addCellIntMetadata |
| addCellMetadata | Add cell metadata |
| addCellStatistics | addCellStatistics |
| addFeatMetadata | Add feature metadata |
| addFeatsPerc | addFeatsPerc |
| addFeatStatistics | Add feature statistics |
| addGeneMetadata | Add gene metadata |
| addGenesPerc | addGenesPerc |
| addGeneStatistics | Add gene statistics |
| addGiottoImage | addGiottoImage |
| addGiottoImageMG | addGiottoImageMG |
| addGiottoImageToSpatPlot | addGiottoImageToSpatPlot |
| addGiottoLargeImage | addGiottoLargeImage |
| addGiottoPoints | Add giotto points object to giotto object |
| addGiottoPoints3D | Add sub cellular 3D coordinates to Giotto object |
| addGiottoPolygons | Add giotto polygons to giotto object |
| addHMRF | addHMRF |
| add_img_array_alpha | Add alpha channel to image array |
| addNetworkLayout | addNetworkLayout |
| addPolygonCells | Add corresponding polygon IDs to cell metadata |
| addSpatialCentroidLocations | addSpatialCentroidLocations |
| addSpatialCentroidLocationsLayer | addSpatialCentroidLocationsLayer |
| addStatistics | addStatistics |
| adjustGiottoMatrix | Adjust expression values |
| aes_string2 | aes_string2 |
| aggregateStacks | aggregateStacks |
| aggregateStacksExpression | aggregateStacksExpression |
| aggregateStacksLocations | aggregateStacksLocations |
| aggregateStacksPolygonOverlaps | aggregateStacksPolygonOverlaps |
| aggregateStacksPolygons | aggregateStacksPolygons |
| aggregateStacksPolygonsOLD | aggregateStacksPolygonsOLD |
| all_plots_save_function | all_plots_save_function |
| anndataToGiotto | Convert anndata to Giotto |
| annotateGiotto | Annotate giotto clustering |
| annotateSpatialGrid | annotateSpatialGrid |
| annotateSpatialNetwork | annotateSpatialNetwork |
| annotate_spatlocs_with_spatgrid_2D | annotate_spatlocs_with_spatgrid_2D |
| annotate_spatlocs_with_spatgrid_3D | annotate_spatlocs_with_spatgrid_3D |
| average_feat_feat_expression_in_groups | average_feat_feat_expression_in_groups |
| binSpect | binSpect |
| binSpectMulti | binSpectMulti |
| binSpectMultiMatrix | binSpectMultiMatrix |
| binSpectSingle | binSpectSingle |
| binSpectSingleMatrix | binSpectSingleMatrix |
| box_chars | Box characters |
| calc_cov_group_HVF | calc_cov_group_HVF |
| calc_cov_loess_HVF | calc_cov_loess_HVF |
| calc_spatial_enrichment_DT | calc_spatial_enrichment_DT |
| calc_spatial_enrichment_matrix | calc_spatial_enrichment_matrix |
| calc_spatial_enrichment_minimum | calc_spatial_enrichment_minimum |
| calculate_centroids_polygons | Calculate polygon centroids |
| calculate_distance_and_weight | calculate_distance_and_weight |
| calculateHVF | calculateHVF |
| calculateHVG | calculateHVG |
| calculateMetaTable | calculateMetaTable |
| calculateMetaTableCells | calculateMetaTableCells |
| calculateOverlapParallel | calculateOverlapParallel |
| calculateOverlapPolygonImages | calculateOverlapPolygonImages |
| calculateOverlapRaster | calculateOverlapRaster |
| calculateOverlapSerial | calculateOverlapSerial |
| calc_var_HVF | calc_var_HVF |
| cal_diff_per_interaction | cal_diff_per_interaction |
| cal_expr_residual | cal_expr_residual |
| cellMetaObj-class | S4 cellMetaObj |
| cellProximityBarplot | cellProximityBarplot |
| cellProximityEnrichment | cellProximityEnrichment |
| cellProximityEnrichmentEachSpot | cellProximityEnrichmentEachSpot |
| cellProximityEnrichmentSpots | cellProximityEnrichmentSpots |
| cellProximityHeatmap | cellProximityHeatmap |
| cellProximityNetwork | cellProximityNetwork |
| cellProximitySpatPlot | cellProximitySpatPlot |
| cellProximitySpatPlot2D | cellProximitySpatPlot2D |
| cellProximitySpatPlot3D | cellProximitySpatPlot3D |
| cell_proximity_spots | cell_proximity_spots |
| cell_proximity_spots_external | cell_proximity_spots_external |
| cell_proximity_spots_internal | cell_proximity_spots_internal |
| cellProximityVisPlot | cellProximityVisPlot |
| cellProximityVisPlot_2D_ggplot | cellProximityVisPlot_2D_ggplot |
| cellProximityVisPlot_2D_plotly | cellProximityVisPlot_2D_plotly |
| cellProximityVisPlot_3D_plotly | cellProximityVisPlot_3D_plotly |
| centroids-generic | centroids-generic |
| changeGiottoInstructions | Change giotto instruction(s) associated with giotto object |
| changeImageBg | changeImageBg |
| check_cell_meta_obj | Check cell metadata object |
| check_dim_obj | Check dimObj |
| check_expr_obj | Check exprObj |
| check_feat_meta_obj | Check feature metadata object |
| checkGiottoEnvironment | checkGiottoEnvironment |
| check_github_suite_ver | Check for updates to Giotto Suite |
| check_py_for_scanpy | Check Scanpy Installation |
| check_spat_grid_obj | Check spatialGridObj |
| check_spatial_location_data | Check spatial location data |
| check_spat_locs_obj | Check spatLocsObj |
| check_spat_net_obj | Check spatialNetworkObj |
| circleVertices | Generate circle polygon vertices |
| clusterCells | clusterCells |
| cluster_enrich_analysis | cluster_enrich_analysis |
| clusterSpatialCorFeats | clusterSpatialCorFeats |
| clusterSpatialCorGenes | clusterSpatialCorGenes |
| colMeans_flex | colMeans_flex |
| color_tag | Colorize print text |
| colSums_flex | colSums_flex |
| combCCcom | combCCcom |
| combineCellData | combineCellData |
| combineCellProximityGenes | combineCellProximityGenes |
| combineCPG | combineCPG |
| combineFeatureData | combineFeatureData |
| combineFeatureOverlapData | combineFeatureOverlapData |
| combineICF | combineICF |
| combineICG | combineICG |
| combineInteractionChangedFeats | combineInteractionChangedFeats |
| combineInteractionChangedFeatures_per_interaction | combineInteractionChangedFeatures_per_interaction |
| combineInteractionChangedGenes | combineInteractionChangedGenes |
| combine_matrices | combine_matrices |
| combineMetadata | combineMetadata |
| combine_polygons | combine_polygons |
| combineSpatialCellFeatureInfo | combineSpatialCellFeatureInfo |
| combineSpatialCellMetadataInfo | combineSpatialCellMetadataInfo |
| combine_spatlocs | combine_spatlocs |
| combine_stack_spatVectors | combine_stack_spatVectors |
| compareCellAbundance | Compare cell types percent per polygon |
| comparePolygonExpression | Compare gene expression between polygon areas |
| compatible_spatial_network | Compatible spatial network |
| convertEnsemblToGeneSymbol | convertEnsemblToGeneSymbol |
| convertGiottoLargeImageToMG | convertGiottoLargeImageToMG |
| convert_mgImage_to_array_DT | convert_mgImage_to_array_DT |
| convert_to_full_spatial_network | convert_to_full_spatial_network |
| convert_to_reduced_spatial_network | convert_to_reduced_spatial_network |
| coordDataDT-class | Basic class for classes with coordinate information |
| copy-generic | Copy an entire object |
| cor_flex | cor_flex |
| create_2d_mesh_grid_line_obj | create_2d_mesh_grid_line_obj |
| create_average_detection_DT | create_average_detection_DT |
| create_average_DT | create_average_DT |
| createCellMetaObj | Create S4 cellMetaObj |
| create_cell_type_random_cell_IDs | create_cell_type_random_cell_IDs |
| create_cluster_matrix | create_cluster_matrix |
| createCrossSection | createCrossSection |
| create_crossSection_object | create_crossSection_object |
| create_delaunayNetwork2D | create_delaunayNetwork2D |
| create_delaunayNetwork3D | create_delaunayNetwork3D |
| create_delaunayNetwork_deldir | create_delaunayNetwork_deldir |
| create_delaunayNetwork_geometry | create_delaunayNetwork_geometry |
| create_delaunayNetwork_geometry_3D | create_delaunayNetwork_geometry_3D |
| create_delaunayNetwork_RTriangle | create_delaunayNetwork_RTriangle |
| createDimObj | Create S4 dimObj |
| createExprObj | Create S4 exprObj |
| createFeatMetaObj | Create S4 featMetaObj |
| create_featureNetwork_object | Create feature network object |
| create_genes_to_use_matrix | create_genes_to_use_matrix |
| createGiottoCosMxObject | Create Nanostring CosMx Giotto Object |
| createGiottoCosMxObject_aggregate | Load and create a CosMx Giotto object from aggregate info |
| createGiottoCosMxObject_all | Load and create a CosMx Giotto object from subcellular and... |
| createGiottoCosMxObject_subcellular | Load and create a CosMx Giotto object from subcellular info |
| createGiottoImage | createGiottoImage |
| createGiottoImageOLD | createGiottoImageOLD |
| createGiottoInstructions | Create instructions for giotto functions |
| createGiottoLargeImage | createGiottoLargeImage |
| createGiottoLargeImageList | createGiottoLargeImageList |
| createGiottoMerscopeObject | Create Vizgen MERSCOPE Giotto Object |
| createGiottoObject | Create a giotto object |
| createGiottoObjectSubcellular | Create a giotto object from subcellular data |
| createGiottoPoints | Create giotto points object |
| create_giotto_points_object | Create giotto points object |
| create_giotto_polygon_object | Create a giotto polygon object |
| createGiottoPolygonsFromDfr | Create giotto polygons from dataframe |
| createGiottoPolygonsFromMask | Create giotto polygons from mask file |
| createGiottoVisiumObject | Create a giotto object from 10x visium data |
| createGiottoXeniumObject | Create 10x Xenium Giotto Object |
| createGiottoXeniumObject_aggregate | Create a Xenium Giotto object from aggregate info |
| createGiottoXeniumObject_subcellular | Create a Xenium Giotto object from subcellular info |
| createHeatmap_DT | createHeatmap_DT |
| create_jackstrawplot | create_jackstrawplot |
| create_KNNnetwork_dbscan | create_KNNnetwork_dbscan |
| create_mesh_grid_lines | create_mesh_grid_lines |
| createMetafeats | createMetafeats |
| createMetagenes | Create metagenes |
| createNearestNetObj | Create S4 nnNetObj |
| createNearestNetwork | createNearestNetwork |
| create_screeplot | create_screeplot |
| create_segm_polygons | Create segmentation polygons |
| create_spat_enr_obj | Create S4 spatEnrObj |
| create_spat_grid_obj | Create S4 spatialGridObj |
| createSpatialDefaultGrid | createSpatialDefaultGrid |
| createSpatialDelaunayNetwork | Create a spatial Delaunay network |
| createSpatialEnrich | createSpatialEnrich |
| createSpatialFeaturesKNNnetwork | Create kNN spatial feature network |
| createSpatialFeaturesKNNnetwork_dbscan | Create kNN spatial feature network using dbscan |
| createSpatialGrid | createSpatialGrid |
| create_spatialGrid_default_2D | create_spatialGrid_default_2D |
| create_spatialGrid_default_3D | create_spatialGrid_default_3D |
| createSpatialKNNnetwork | createSpatialKNNnetwork |
| createSpatialNetwork | createSpatialNetwork |
| createSpatialWeightMatrix | Create a spatial weight matrix |
| create_spat_locs_obj | Create S4 spatLocsObj |
| createSpatNetObj | Create S4 spatialNetworkObj |
| create_spatvector_object_from_dfr | Create terra spatvector object from a data.frame |
| create_terra_spatRaster | Load image as a terra spatRaster object |
| cropGiottoLargeImage | Crop a giotto largeImage object |
| crossSectionGenePlot | crossSectionGenePlot |
| crossSectionGenePlot3D | crossSectionGenePlot3D |
| crossSectionPlot | crossSectionPlot |
| crossSectionPlot3D | crossSectionPlot3D |
| data_access_params | data_access_params |
| data.table-class | data.table S4 class for method dispatch |
| decide_cluster_order | decide_cluster_order |
| degrees | Radian/degree conversions |
| density_giottoLargeImage | Plot smoothed curve of giotto largeImage intensity values |
| depth | Find depth of subnesting |
| detectSpatialCorFeats | detectSpatialCorFeats |
| detectSpatialCorFeatsMatrix | detectSpatialCorFeatsMatrix |
| detectSpatialCorGenes | detectSpatialCorGenes |
| detectSpatialPatterns | detectSpatialPatterns |
| determine_cores | determine_cores |
| dimCellPlot | dimCellPlot |
| dimCellPlot2D | dimCellPlot2D |
| dimFeatPlot2D | dimFeatPlot2D |
| dimGenePlot | dimGenePlot |
| dimGenePlot2D | dimGenePlot2D |
| dimGenePlot3D | dimGenePlot3D |
| dimObj-class | S4 dimObj Class |
| dimPlot | dimPlot |
| dimPlot2D | Plot dimension reduction 2D |
| dimPlot_2D_plotly | dimPlot_2D_plotly |
| dimPlot2D_single | dimPlot2D_single |
| dimPlot3D | dimPlot3D |
| dimPlot_3D_plotly | dimPlot_3D_plotly |
| dims-generic | Dimensions of giotto objects |
| distGiottoImage | Plot distribution of image intensity values |
| do_cell_proximity_test | Do cell proximity test |
| do_cell_proximity_test_spot | do_cell_proximity_test_spot |
| doCellSegmentation | doCellSegmentation |
| do_gpoly | do_gpoly |
| doHclust | doHclust |
| doHMRF | doHMRF |
| doKmeans | doKmeans |
| doLeidenCluster | doLeidenCluster |
| doLeidenSubCluster | doLeidenSubCluster |
| do_limmatest | do_limmatest |
| doLouvainCluster | doLouvainCluster |
| doLouvainCluster_community | doLouvainCluster_community |
| doLouvainCluster_multinet | doLouvainCluster_multinet |
| doLouvainSubCluster | doLouvainSubCluster |
| doLouvainSubCluster_community | doLouvainSubCluster_community |
| doLouvainSubCluster_multinet | doLouvainSubCluster_multinet |
| do_multi_permuttest_random | do_multi_permuttest_random |
| do_multi_permuttest_random_spot | do_multi_permuttest_random_spot |
| do_page_permutation | do_page_permutation |
| do_permuttest_original | do_permuttest_original |
| do_permuttest_original_spot | do_permuttest_original_spot |
| do_permuttest_random | do_permuttest_random |
| do_permuttest_random_spot | do_permuttest_random_spot |
| do_permuttest_spot | do_permuttest_spot |
| doRandomWalkCluster | doRandomWalkCluster |
| do_rank_permutation | do_rank_permutation |
| doScrubletDetect | doScrubletDetect |
| doSNNCluster | doSNNCluster |
| do_spatial_grid_averaging | do_spatial_grid_averaging |
| do_spatial_knn_smoothing | do_spatial_knn_smoothing |
| dot-h5_read_bare | Read dataset from opened HDF5 with C functions |
| do_ttest | do_ttest |
| do_wilctest | do_wilctest |
| DT_removeNA | DT_removeNA |
| dt_to_matrix | dt_to_matrix |
| dt_to_spatVector_points | Convert point data data.table to spatVector |
| dt_to_spatVector_polygon | Convert data.table to polygon spatVector |
| enrData-class | enrData |
| enrich_analysis | enrich_analysis |
| enrich_deconvolution | enrich_deconvolution |
| estimateCellCellDistance | estimateCellCellDistance |
| estimateImageBg | estimateImageBg |
| evaluate_provided_spatial_locations | Evaluate provided spatial locations |
| expand_feature_info | expand_feature_info |
| exportGiottoViewer | exportGiottoViewer |
| exprCellCellcom | exprCellCellcom |
| exprData-class | Basic class for classes with expression information |
| exprObj-class | S4 exprObj |
| extended_gini_fun | extended_gini_fun |
| extend_vector | extend_vector |
| extract-methods | Extract or replace parts of an object |
| fDataDT | fDataDT |
| featData-class | Basic class for classes with feature information |
| featExpDWLS | featExpDWLS |
| featMetaObj-class | S4 featMetaObj |
| featType-generic | Feature type information |
| featureNetwork-class | S4 giotto feature network Class |
| filterCellProximityGenes | filterCellProximityGenes |
| filterCombinations | filterCombinations |
| filterCPG | filterCPG |
| filterDistributions | filterDistributions |
| filterGiotto | filterGiotto |
| filterICF | filterICF |
| filterICFSpot | filterICFSpot |
| filterICG | filterICG |
| filterInteractionChangedFeats | filterInteractionChangedFeats |
| filterInteractionChangedGenes | filterInteractionChangedGenes |
| filter_network | filter_network |
| findCellProximityFeats_per_interaction | findCellProximityFeats_per_interaction |
| findCellProximityGenes | findCellProximityGenes |
| findCPG | findCPG |
| find_dampening_constant | find_dampening_constant |
| findGiniMarkers | findGiniMarkers |
| findGiniMarkers_one_vs_all | findGiniMarkers_one_vs_all |
| find_grid_2D | find_grid_2D |
| find_grid_3D | find_grid_3D |
| find_grid_x | find_grid_x |
| find_grid_y | find_grid_y |
| find_grid_z | find_grid_z |
| findICF | findICF |
| findICF_per_interaction_spot | findICF_per_interaction_spot |
| findICFSpot | findICFSpot |
| findICG | findICG |
| findInteractionChangedFeats | findInteractionChangedFeats |
| findInteractionChangedGenes | findInteractionChangedGenes |
| findMarkers | findMarkers |
| findMarkers_one_vs_all | findMarkers_one_vs_all |
| findMastMarkers | findMastMarkers |
| findMastMarkers_one_vs_all | findMastMarkers_one_vs_all |
| findNetworkNeighbors | Find network neighbors |
| findScranMarkers | findScranMarkers |
| findScranMarkers_one_vs_all | findScranMarkers_one_vs_all |
| find_terra_writeRaster_dataType | find_terra_writeRaster_dataType |
| find_x_y_ranges | find_x_y_ranges |
| fix_multipart_geoms | Split multi-part polygons |
| flex_lapply | flex_lapply |
| fread_colmatch | Fread rows based on column matches |
| FSV_show | FSV_show |
| gefToGiotto | Convert gef to Giotto |
| general_save_function | general_save_function |
| get10Xmatrix | get10Xmatrix |
| get10Xmatrix_h5 | get10Xmatrix_h5 |
| get10XmatrixOLD | get10XmatrixOLD |
| get_adj_rescale_img | get_adj_rescale_img |
| getBalancedSpatCoexpressionFeats | getBalancedSpatCoexpressionFeats |
| get_cell_id | Get cell IDs for a given spatial unit |
| get_cell_metadata | Get cell metadata |
| getCellMetadata | getCellMetadata |
| getCellsFromPolygon | Get cells located within the polygons area |
| getClusterSimilarity | getClusterSimilarity |
| get_cross_section_coordinates | get_cross_section_coordinates |
| getDendrogramSplits | getDendrogramSplits |
| get_dimReduction | Get dimension reduction |
| getDimReduction | Get dimension reduction |
| get_distance | get_distance |
| getDistinctColors | getDistinctColors |
| getExpression | Get expression values |
| get_feat_id | Get feat IDs for a given feature type |
| get_feature_info | Get feature info |
| getFeatureInfo | Get feature info |
| get_feature_metadata | Get feature metadata |
| getFeatureMetadata | getFeatureMetadata |
| getGEFtxCoords | getGEFtxCoords |
| get_giottoImage | Get giotto image object |
| getGiottoImage | Get giotto image object |
| get_giottoImage_MG | Get _magick_-based giotto 'image' |
| get_GiottoLargeImage | Get _terra_-based giotto 'largeImage' |
| get_img_corners | get_img_corners |
| get_img_minmax | get_img_minmax |
| get_multiomics | Get multiomics integration results |
| getMultiomics | Get multiomics integration results |
| getNearestNetwork | Get nearest neighbor network |
| get_NearestNetwork | Get nearest network |
| get_os | get_os |
| get_polygon_info | Get polygon info |
| getPolygonInfo | Get polygon info |
| getRainbowColors | getRainbowColors |
| get_sectionThickness | get_sectionThickness |
| get_spatial_enrichment | Get spatial enrichment |
| getSpatialEnrichment | Get spatial enrichment |
| get_spatialGrid | Get spatial grid |
| getSpatialGrid | Get spatial grid |
| get_spatial_locations | Get spatial locations |
| getSpatialLocations | Get spatial locations |
| get_spatialNetwork | Get spatial network |
| getSpatialNetwork | Get spatial network |
| ggplot_save_function | ggplot_save_function |
| giotto_alloc_dt_slots | Over-allocation for giotto DT-based info |
| giotto-class | S4 giotto Class |
| giottoImage-class | S4 giottoImage Class |
| giotto_lapply | giotto_lapply |
| giottoLargeImage-class | S4 giottoLargeImage Class |
| giotto_point | giotto_point |
| giottoPoints-class | S4 giotto points Class |
| giottoPolygon-class | S4 giotto polygon Class |
| giottoToAnnData | Convert Giotto to anndata |
| giottoToSeurat | Convert Giotto to Seurat |
| giottoToSpatialExperiment | Utility function to convert a Giotto object to a... |
| gpoly_from_dfr_smoothed_wrapped | Polygon creation and smoothing for parallel |
| heatmSpatialCorFeats | heatmSpatialCorFeats |
| heatmSpatialCorGenes | heatmSpatialCorGenes |
| hexVertices | Generate regular hexagon vertices |
| hyperGeometricEnrich | hyperGeometricEnrich |
| identify_background_range_polygons | Identify background range polygons |
| init_cell_metadata | Initialize cell metadata slot |
| init_feat_metadata | Initialize feature metadata slot |
| insertCrossSectionGenePlot3D | insertCrossSectionGenePlot3D |
| insertCrossSectionSpatPlot3D | insertCrossSectionSpatPlot3D |
| install_giotto_environment | install_giotto_environment |
| installGiottoEnvironment | installGiottoEnvironment |
| install_giotto_environment_specific | install_giotto_environment_specific |
| instructions-generic | Access giotto instructions |
| jackstrawPlot | jackstrawPlot |
| joinGiottoObjects | Join giotto objects |
| kmeans_arma_binarize | kmeans_arma_binarize |
| kmeans_arma_subset_binarize | kmeans_arma_subset_binarize |
| kmeans_binarize | kmeans_binarize |
| kmeans_binarize_wrapper | kmeans_binarize_wrapper |
| lapply_flex | lapply_flex |
| libNorm_giotto | Normalize for library size |
| list_cell_id_names | List cell ID names |
| list_cell_metadata | list_cell_metadata |
| list_dim_reductions | list_dim_reductions |
| list_dim_reductions_names | list_dim_reductions_names |
| list_expression | list_expression |
| list_expression_names | list_expression_names |
| list_feat_id_names | List feat ID names |
| list_feat_metadata | list_feat_metadata |
| list_feature_info | list_feature_info |
| list_feature_info_names | list_feature_info_names |
| list_giotto_data | list_giotto_data |
| list_images | list_images |
| list_images_names | list_images_names |
| list_nearest_networks | list_nearest_networks |
| list_nearest_networks_names | list_nearest_networks_names |
| list_spatial_enrichments | list_spatial_enrichments |
| list_spatial_enrichments_names | list_spatial_enrichments_names |
| list_spatial_grids | list_spatial_grids |
| list_spatial_grids_names | list_spatial_grids_names |
| list_spatial_info | list_spatial_info |
| list_spatial_info_names | list_spatial_info_names |
| list_spatial_locations | list_spatial_locations |
| list_spatial_locations_names | list_spatial_locations_names |
| list_spatial_networks | list_spatial_networks |
| list_spatial_networks_names | list_spatial_networks_names |
| load_cosmx_folder_aggregate | Load CosMx folder aggregate info |
| load_cosmx_folder_subcellular | Load CosMx folder subcellular info |
| loadGiotto | loadGiotto |
| loadHMRF | loadHMRF |
| load_merscope_folder | Load MERSCOPE data from folder |
| load_xenium_folder | Load xenium data from folder |
| logNorm_giotto | logNorm_giotto |
| makeSignMatrixDWLS | makeSignMatrixDWLS |
| makeSignMatrixDWLSfromMatrix | makeSignMatrixDWLSfromMatrix |
| makeSignMatrixPAGE | makeSignMatrixPAGE |
| makeSignMatrixRank | makeSignMatrixRank |
| make_simulated_network | make_simulated_network |
| mean_expr_det_test | mean_expr_det_test |
| mean_flex | mean_flex |
| mergeClusters | mergeClusters |
| merge_spatial_locs_feat_info | merge_spatial_locs_feat_info |
| metaData-class | Basic class for classes with metadata information |
| miscData-class | Basic class for additional miscellaneous information |
| my_arowMeans | my_arowMeans |
| mygini_fun | mygini_fun |
| my_growMeans | my_growMeans |
| my_rowMeans | my_rowMeans |
| nnDT_to_kNN | nnDT_to_kNN |
| nnNetObj-class | S4 nnNetObj |
| node_clusters | node_clusters |
| normalizeGiotto | normalizeGiotto |
| nullOrChar-class | NULL or char class union |
| nullOrDatatable-class | NULL or data.table class union |
| nullOrList-class | NULL or list class union |
| objHistory | Giotto object history |
| objName-generic | Giotto object name information |
| optimize_deconvolute_dwls | optimize_deconvolute_dwls |
| optimize_solveDampenedWLS | optimize_solveDampenedWLS |
| OR_test_fnc | OR_test_fnc |
| overlapImagesToMatrix | overlapImagesToMatrix |
| overlap_points_per_polygon | Overlap points per polgyon |
| overlap_points_per_polygon_wrapped | Overlap points per polygon - wrapped |
| overlap_points_single_polygon | Overlap points - single polygon |
| overlaps-generic | overlaps-generic |
| overlapToMatrix | overlapToMatrix |
| overlapToMatrixMultiPoly | overlapToMatrixMultiPoly |
| package_check | package_check |
| PAGE_DT_method | PAGE_DT_method |
| PAGEEnrich | PAGEEnrich |
| pca_giotto | pca_giotto |
| pDataDT | pDataDT |
| pipe | Pipe operator |
| plot_auto_largeImage_resample | Optimized largeImage resampling |
| plotCCcomDotplot | plotCCcomDotplot |
| plotCCcomHeatmap | plotCCcomHeatmap |
| plot_cell_polygon_layer | Plot cell polygon layer |
| plotCellProximityFeats | plotCellProximityFeats |
| plotCellProximityFeatSpot | plotCellProximityFeatSpot |
| plotCellProximityGenes | plotCellProximityGenes |
| plotCombineCCcom | plotCombineCCcom |
| plotCombineCellCellCommunication | plotCombineCellCellCommunication |
| plotCombineCellProximityGenes | plotCombineCellProximityGenes |
| plotCombineCPG | plotCombineCPG |
| plotCombineICF | plotCombineICF |
| plotCombineICG | plotCombineICG |
| plotCombineInteractionChangedFeats | plotCombineInteractionChangedFeats |
| plotCombineInteractionChangedGenes | plotCombineInteractionChangedGenes |
| plotCPF | plotCPF |
| plotCPG | plotCPG |
| plot_feature_hexbin_layer | plot_feature_hexbin_layer |
| plot_feature_points_layer | plot_feature_points_layer |
| plot_feature_raster_density_layer | plot_feature_raster_density_layer |
| plot-generic | Preview a Giotto spatial object |
| plotGiottoImage | Plot a giotto image object |
| plot_giottoImage_MG | plot_giottoImage_MG |
| plot_giottoLargeImage | plot_giottoLargeImage |
| plotHeatmap | plotHeatmap |
| plotICF | Plot interaction changed features |
| plotICFSpot | plotICFSpot |
| plotICG | plotICG |
| plotInteractionChangedFeats | Plot interaction changed features |
| plotInteractionChangedGenes | Plot interaction changed genes |
| plotInteractivePolygons | Select image regions by plotting interactive polygons |
| plotly_axis_scale_2D | plotly_axis_scale_2D |
| plotly_axis_scale_3D | plotly_axis_scale_3D |
| plotly_grid | plotly_grid |
| plotly_network | plotly_network |
| plotMetaDataCellsHeatmap | plotMetaDataCellsHeatmap |
| plotMetaDataHeatmap | plotMetaDataHeatmap |
| plot_params | plot_params |
| plotPCA | plotPCA |
| plotPCA_2D | plotPCA_2D |
| plotPCA_3D | plotPCA_3D |
| plotPolygons | Plot stored polygons |
| plotRankSpatvsExpr | plotRankSpatvsExpr |
| plotRecovery | plotRecovery |
| plotRecovery_sub | plotRecovery_sub |
| plotStatDelaunayNetwork | plotStatDelaunayNetwork |
| plotTSNE | plotTSNE |
| plotTSNE_2D | plotTSNE_2D |
| plotTSNE_3D | plotTSNE_3D |
| plotUMAP | plotUMAP |
| plotUMAP_2D | plotUMAP_2D |
| plotUMAP_3D | plotUMAP_3D |
| polygon_to_raster | Convert polygon to raster |
| polygon_to_raster_OLD | Convert polygon to raster |
| polyStamp | Spatial polygons stamp |
| print_leaf | Hierarchical tree printing |
| processGiotto | processGiotto |
| projection_fun | projection_fun |
| provData-class | Basic class for classes with provenance information. |
| prov-generic | Provenance information |
| prov_match | Check provenance info matches across list of S4 subobjects |
| rank_binarize | rank_binarize |
| rank_binarize_wrapper | rank_binarize_wrapper |
| rankEnrich | rankEnrich |
| rankSpatialCorGroups | rankSpatialCorGroups |
| rbind2_giotto_polygon_hetero | Append giotto polygons of different names |
| rbind2_giotto_polygon_homo | Append giotto polygons of the same name |
| rbind-generic | Combine objects by rows (Giotto-related) |
| read_cell_metadata | Read cell metadata |
| read_cosmx_folder | Read a structured CosMx folder |
| read_crossSection | read_crossSection |
| read_data_folder | Read a structured folder of exported data |
| readDimReducData | Read dimensional reduction data |
| readExprData | Read expression data |
| readExprMatrix | Read expression matrix |
| readFeatData | Read feature information |
| read_feature_metadata | Read feature metadata |
| readGiottoInstructions | Read giotto instructions associated with giotto object |
| readNearestNetData | Read nearest neighbor network data |
| readPolygonData | Read list of polygons information |
| readPolygonFilesVizgen | readPolygonFilesVizgen |
| readPolygonFilesVizgenHDF5 | readPolygonFilesVizgenHDF5 |
| readPolygonFilesVizgenHDF5_old | readPolygonFilesVizgenHDF5 |
| readSpatEnrichData | Read spatial enrichment |
| readSpatLocsData | Read spatial location data |
| readSpatNetData | Read spatial networks |
| read_xenium_folder | Read a structured xenium folder |
| reconnectGiottoImage | Reconnect images with dead pointers |
| reconnect_giottoImage_MG | reconnect_giottoImage_MG |
| reconnect_giottoLargeImage | reconnect_giottoLargeImage |
| reconnect_image_object | reconnect_image_object |
| rectVertices | Generate rectangular polygon vertices |
| reg_img_minmax_finder | reg_img_minmax_finder |
| registerGiottoObjectList | registerGiottoObjectList |
| registerGiottoObjectListFiji | registerGiottoObjectListFiji |
| registerGiottoObjectListRvision | registerGiottoObjectListRvision |
| registerImagesFIJI | registerImagesFIJI |
| removeCellAnnotation | Remove cell annotation |
| removeFeatAnnotation | Remove feature annotation |
| removeGiottoEnvironment | removeGiottoEnvironment |
| replaceGiottoInstructions | Replace all giotto instructions in giotto object |
| rescale_polygons | rescale polygons |
| rescalePolygons | rescalePolygons |
| reshape_to_data_point | reshape_to_data_point |
| reshape_to_mesh_grid_obj | reshape_to_mesh_grid_obj |
| return_giotto_environment_path | return_giotto_environment_path |
| return_giotto_environment_path_executable | return_giotto_environment_path_executable |
| rigid_transform_spatial_locations | rigid_transform_spatial_locations |
| rna_osmfish_normalization | RNA osmfish normalization |
| rna_pears_resid_normalization | RNA pearson residuals normalization |
| rna_standard_normalization | RNA standard normalization |
| rotate_spatial_locations | Rotate spatial locations |
| rowMeans_flex | rowMeans_flex |
| row-plus-colnames-generic | Row and column names |
| rowSums_flex | rowSums_flex |
| runDWLSDeconv | runDWLSDeconv |
| runFijiMacro | Find Fiji location |
| runGiottoHarmony | runGiottoHarmony |
| runHyperGeometricEnrich | runHyperGeometricEnrich |
| runIntegratedUMAP | Run integrated UMAP |
| runPAGEEnrich | runPAGEEnrich |
| runPAGEEnrich_OLD | runPAGEEnrich_OLD |
| runPatternSimulation | runPatternSimulation |
| runPCA | runPCA |
| runPCA_BiocSingular | runPCA_BiocSingular |
| runPCA_factominer | runPCA_factominer |
| runPCA_prcomp_irlba | runPCA_prcomp_irlba |
| runRankEnrich | runRankEnrich |
| run_spat_autocor_global | run_spat_autocor_global |
| run_spat_autocor_local | run_spat_autocor_local |
| runSpatialDeconv | runSpatialDeconv |
| runSpatialEnrich | runSpatialEnrich |
| run_spatial_sim_tests_multi | run_spatial_sim_tests_multi |
| run_spatial_sim_tests_one_rep | run_spatial_sim_tests_one_rep |
| runtSNE | Run tSNE dimensional reduction |
| runUMAP | Run UMAP dimension reduction |
| runWNN | Multi omics integration with WNN |
| S3toS4dimObj | Dimension reductions |
| S3toS4spatGridObj | Spatially Binned Data |
| S3toS4spatNetObj | Spatial Networks |
| saveGiotto | saveGiotto |
| scale_spatial_locations | Scale spatial locations |
| screePlot | screePlot |
| select_gimage | select_gimage |
| selectPatternGenes | selectPatternGenes |
| set_cell_id | Set cell IDs for a given spatial unit |
| set_cell_metadata | Set cell metadata |
| setCellMetadata | Set cell metadata |
| set_default_cow_n_col | Set default ncols in plotting grid |
| set_default_feat_type | set_default_feat_type |
| set_default_spat_unit | set_default_spat_unit |
| set_dimReduction | Set dimension reduction |
| setDimReduction | Set dimension reduction data |
| setExpression | Set expression data |
| set_expression_values | Set expression values |
| set_feat_id | Set feat IDs for a given feature type |
| set_feature_info | Set feature info |
| setFeatureInfo | Set feature info |
| setFeatureMetadata | Set feature metadata |
| set_giottoImage | Set giotto image object |
| setGiottoImage | Set giotto image object |
| set_giottoImage_MG | Set _magick_-based giotto 'image' |
| set_giottoLargeImage | Set _terra_-based giotto 'largeImage' |
| set_giotto_python_path | set_giotto_python_path |
| set_multiomics | Set multiomics integration results |
| setMultiomics | Set multiomics integration results |
| setNearestNetwork | Set nearest neighbor network |
| set_NearestNetwork | Set nearest network |
| set_polygon_info | Set polygon info |
| setPolygonInfo | Set polygon info |
| set_spatial_enrichment | Set spatial enrichment |
| setSpatialEnrichment | Set spatial enrichment |
| set_spatialGrid | Set spatial grid |
| setSpatialGrid | Set spatial grid |
| set_spatial_locations | Set spatial locations |
| setSpatialLocations | Set spatial locations |
| set_spatialNetwork | Set spatial network |
| setSpatialNetwork | Set spatial network |
| seuratToGiotto | Convert a Seurat object to a Giotto object |
| seuratToGiotto_OLD | seuratToGiotto_OLD |
| shift_spatial_locations | Shift spatial locations |
| shift_spatial_network | Shift spatial network |
| showClusterDendrogram | showClusterDendrogram |
| showClusterHeatmap | showClusterHeatmap |
| showGiottoCellMetadata | showGiottoCellMetadata |
| showGiottoDimRed | showGiottoDimRed |
| showGiottoExpression | showGiottoExpression |
| showGiottoFeatInfo | showGiottoFeatInfo |
| showGiottoFeatMetadata | showGiottoFeatMetadata |
| showGiottoImageNames | showGiottoImageNames |
| showGiottoInstructions | Show giotto instructions associated with giotto object |
| showGiottoNearestNetworks | showGiottoNearestNetworks |
| showGiottoSpatEnrichments | showGiottoSpatEnrichments |
| showGiottoSpatGrids | showGiottoSpatGrids |
| showGiottoSpatialInfo | showGiottoSpatialInfo |
| showGiottoSpatLocs | showGiottoSpatLocs |
| showGiottoSpatNetworks | showGiottoSpatNetworks |
| showGrids | Show Spatial Grids |
| show-methods | show method for giotto class |
| showNetworks | Show networks |
| showPattern | showPattern |
| showPattern2D | showPattern2D |
| showPattern3D | showPattern3D |
| showPatternGenes | showPatternGenes |
| showProcessingSteps | showProcessingSteps |
| showSaveParameters | showSaveParameters |
| showSpatialCorFeats | showSpatialCorFeats |
| showSpatialCorGenes | showSpatialCorGenes |
| signPCA | signPCA |
| silhouetteRank | silhouetteRank |
| silhouetteRankTest | silhouetteRankTest |
| simulateOneGenePatternGiottoObject | simulateOneGenePatternGiottoObject |
| slot | See 'methods::slot' for details. |
| slotNames | See 'methods::slotNames' for details. |
| smoothGiottoPolygons | smoothGiottoPolygons |
| solve_dampened_WLSj | solve_dampened_WLSj |
| solve_OLS_internal | solve_OLS_internal |
| sort_combine_two_DT_columns | sort_combine_two_DT_columns |
| spark | spark |
| spatCellCellcom | spatCellCellcom |
| spatCellCellcomSpots | spatCellCellcomSpots |
| spatCellPlot | spatCellPlot |
| spatCellPlot2D | spatCellPlot2D |
| spatData-class | Basic class for classes with spatial information |
| spatDeconvPlot | spatDeconvPlot |
| spatDimCellPlot | spatDimCellPlot |
| spatDimCellPlot2D | spatDimCellPlot2D |
| spatDimFeatPlot2D | spatDimFeatPlot2D |
| spatDimGenePlot | spatDimGenePlot |
| spatDimGenePlot2D | spatDimGenePlot2D |
| spatDimGenePlot3D | spatDimGenePlot3D |
| spatDimPlot | spatDimPlot |
| spatDimPlot2D | spatDimPlot2D |
| spatDimPlot3D | spatDimPlot3D |
| spatEnrObj-class | S4 spatEnrObj Class |
| spatFeatData-class | Superclass for classes that contain both spatial and feature... |
| spatFeatPlot2D | Plot data in physical space 2D |
| spatFeatPlot2D_single | spatFeatPlot2D_single |
| spat_fish_func | spat_fish_func |
| spat_fish_func_DT | spat_fish_func_DT |
| spatGenePlot | spatGenePlot |
| spatGenePlot2D | spatGenePlot2D |
| spatGenePlot3D | spatGenePlot3D |
| spatialAEH | spatialAEH |
| spatialAutoCor | Spatial autocorrelation |
| spatialDE | spatialDE |
| spatialExperimentToGiotto | Utility function to convert a SpatialExperiment object to a... |
| spatialGridObj-class | S4 spatialGridObj Class |
| spatialNetworkObj-class | S4 spatialNetworkObj Class |
| spatIDs-generic | Spatial and feature IDs |
| spatInSituPlotDensity | spatInSituPlotDensity |
| spatInSituPlotDensity_single | spatInSituPlotDensity_single |
| spatInSituPlotHex | spatInSituPlotHex |
| spatInSituPlotHex_single | spatInSituPlotHex_single |
| spatInSituPlotPoints | spatInSituPlotPoints |
| spatLocsObj-class | S4 spatLocsObj Class |
| spatNetwDistributions | spatNetwDistributions |
| spatNetwDistributionsDistance | Plot spatial distance distribution |
| spatNetwDistributionsKneighbors | spatNetwDistributionsKneighbors |
| spat_OR_func | spat_OR_func |
| spat_OR_func_DT | spat_OR_func_DT |
| spatPlot | spatPlot |
| spatPlot2D | spatPlot2D |
| spatPlot_2D_plotly | spatPlot_2D_plotly |
| spatPlot2D_single | spatPlot2D_single |
| spatPlot3D | spatPlot3D |
| spatPlot_3D_plotly | spatPlot_3D_plotly |
| spatShift | Spatially shift an object |
| spatUnit-generic | Spatial unit information |
| spatVector_to_dt | Convert spatVector to data.table |
| spatVector_to_dt2 | Convert spatVector to data.table |
| specific_CCCScores_spots | specific_CCCScores_spots |
| specificCellCellcommunicationScores | specificCellCellcommunicationScores |
| spin-generic | Spin an object |
| spline_poly | Convert spline to polygon |
| split_dendrogram_in_two | split_dendrogram_in_two |
| spot_deconvolution | spot_deconvolution |
| standardise_flex | standardise_flex |
| stitchFieldCoordinates | stitchFieldCoordinates |
| stitchGiottoLargeImage | Stitch multiple giottoLargeImage objects into a single... |
| stitchTileCoordinates | stitchTileCoordinates |
| subClusterCells | subClusterCells |
| subset_cell_metadata | Subset cell metadata |
| subset_feature_metadata | Subset feature metadata |
| subsetGiotto | subsetGiotto |
| subsetGiottoLocs | Subset by spatial locations |
| subsetGiottoLocsMulti | Subset by spatial locations - multi |
| subsetGiottoLocsSubcellular | Subset raw subcellular information by location |
| t_flex | t_flex |
| time_format | Format time for printing |
| trakem2_rigid_transf_extract | trakem2_rigid_transf_extract |
| transform_2d_mesh_to_3d_mesh | transform_2d_mesh_to_3d_mesh |
| transpose-generic | Transpose |
| trendSceek | trendSceek |
| updateGiottoImage | updateGiottoImage |
| updateGiottoImageMG | updateGiottoImageMG |
| updateGiottoLargeImage | updateGiottoLargeImage |
| updateGiottoObject | Update giotto object |
| updateGiottoPointsObject | Update giotto points object |
| updateGiottoPolygonObject | Update giotto polygon object |
| validObject | See 'methods::validObject' for details. |
| viewHMRFresults | viewHMRFresults |
| viewHMRFresults2D | viewHMRFresults2D |
| viewHMRFresults3D | viewHMRFresults3D |
| violinPlot | violinPlot |
| wrap-generic | Wrap giotto terra pointer information |
| wrap_msg | Wrap message |
| wrap_txt | Wrap text |
| writeGiottoLargeImage | writeGiottoLargeImage |
| write_giotto_viewer_annotation | write_giotto_viewer_annotation |
| write_giotto_viewer_dim_reduction | write_giotto_viewer_dim_reduction |
| write_giotto_viewer_numeric_annotation | write_giotto_viewer_numeric_annotation |
| writeHMRFresults | writeHMRFresults |
