Man pages for RubD/Giotto
Spatial Single-Cell Transcriptomics Toolbox
| adapt_aspect_ratio | adapt_aspect_ratio |
| addCellIntMetadata | addCellIntMetadata |
| addCellMetadata | addCellMetadata |
| addCellStatistics | addCellStatistics |
| addGeneMetadata | addGeneMetadata |
| addGenesPerc | addGenesPerc |
| addGeneStatistics | addGeneStatistics |
| addGiottoImage | addGiottoImage |
| addGiottoImageToSpatPlot | addGiottoImageToSpatPlot |
| addHMRF | addHMRF |
| addHMRF_V2 | addHMRF_V2 |
| addNetworkLayout | addNetworkLayout |
| addStatistics | addStatistics |
| adjustGiottoMatrix | adjustGiottoMatrix |
| aes_string2 | aes_string2 |
| all_plots_save_function | all_plots_save_function |
| anndataToGiotto | anndataToGiotto |
| annotateGiotto | annotateGiotto |
| 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_gene_gene_expression_in_groups | average_gene_gene_expression_in_groups |
| binSpect | binSpect |
| binSpectMulti | binSpectMulti |
| binSpectSingle | binSpectSingle |
| 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_distance_and_weight | calculate_distance_and_weight |
| calculateHVG | calculateHVG |
| calculateMetaTable | calculateMetaTable |
| calculateMetaTableCells | calculateMetaTableCells |
| cal_diff_per_interaction | cal_diff_per_interaction |
| cal_expr_residual | cal_expr_residual |
| cellProximityBarplot | cellProximityBarplot |
| cellProximityEnrichment | cellProximityEnrichment |
| cellProximityEnrichmentEachSpot | cellProximityEnrichmentEachSpot |
| cellProximityEnrichmentSpots | cellProximityEnrichmentSpots |
| cellProximityHeatmap | cellProximityHeatmap |
| cellProximityNetwork | cellProximityNetwork |
| cellProximitySpatPlot | cellProximitySpatPlot |
| cellProximitySpatPlot2D | cellProximitySpatPlot2D |
| cellProximitySpatPlot3D | cellProximitySpatPlot2D |
| 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 |
| changeGiottoInstructions | changeGiottoInstructions |
| changeImageBg | changeImageBg |
| checkAndFixSpatialGenes | checkAndFixSpatialGenes |
| checkGiottoEnvironment | checkGiottoEnvironment |
| chooseAvailableSpatialGenes | chooseAvailableSpatialGenes |
| clusterCells | clusterCells |
| cluster_enrich_analysis | cluster_enrich_analysis |
| clusterSpatialCorGenes | clusterSpatialCorGenes |
| colMeans_flex | colMeans_flex |
| colMeans_giotto | colMeans_giotto |
| colSums_flex | colSums_flex |
| colSums_giotto | colSums_giotto |
| combCCcom | combCCcom |
| combineCellProximityGenes | combineCellProximityGenes |
| combineCellProximityGenes_per_interaction | combineCellProximityGenes_per_interaction |
| combineCPG | combineCPG |
| combineICG | combineICG |
| combineInteractionChangedGenes | combineInteractionChangedGenes |
| combineMetadata | combineMetadata |
| convertEnsemblToGeneSymbol | convertEnsemblToGeneSymbol |
| 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 |
| cor_flex | cor_flex |
| cor_giotto | cor_giotto |
| cor_sparse | cor_sparse adapted from wydr package |
| 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 |
| 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 |
| create_dimObject | create_dimObject |
| create_genes_to_use_matrix | create_genes_to_use_matrix |
| createGiottoImage | createGiottoImage |
| createGiottoInstructions | createGiottoInstructions |
| createGiottoObject | create Giotto object |
| createGiottoVisiumObject | createGiottoVisiumObject |
| createHeatmap_DT | createHeatmap_DT |
| create_jackstrawplot | create_jackstrawplot |
| create_KNNnetwork_dbscan | create_KNNnetwork_dbscan |
| create_mesh_grid_lines | create_mesh_grid_lines |
| createMetagenes | createMetagenes |
| createNearestNetwork | createNearestNetwork |
| createRegZStackGobject | createRegZStackGobject |
| create_screeplot | create_screeplot |
| createSpatialDefaultGrid | createSpatialDefaultGrid |
| createSpatialDelaunayNetwork | createSpatialDelaunayNetwork |
| createSpatialEnrich | createSpatialEnrich |
| createSpatialGrid | createSpatialGrid |
| create_spatialGrid_default_2D | create_spatialGrid_default_2D |
| create_spatialGrid_default_3D | create_spatialGrid_default_3D |
| create_spatialGridObject | create_spatialGridObject |
| createSpatialKNNnetwork | createSpatialKNNnetwork |
| createSpatialNetwork | createSpatialNetwork |
| create_spatialNetworkObject | create_spatialNetworkObject |
| crossSectionGenePlot | crossSectionGenePlot |
| crossSectionGenePlot3D | crossSectionGenePlot3D |
| crossSectionPlot | crossSectionPlot |
| crossSectionPlot3D | crossSectionPlot3D |
| decide_cluster_order | decide_cluster_order |
| detectSpatialCorGenes | detectSpatialCorGenes |
| detectSpatialPatterns | detectSpatialPatterns |
| determine_cores | determine_cores |
| dimCellPlot | dimCellPlot |
| dimCellPlot2D | dimCellPlot2D |
| dimGenePlot | dimGenePlot |
| dimGenePlot2D | dimGenePlot2D |
| dimGenePlot3D | dimGenePlot3D |
| dimPlot | dimPlot |
| dimPlot2D | dimPlot2D |
| dimPlot_2D_plotly | dimPlot_2D_plotly |
| dimPlot2D_single | dimPlot2D_single |
| dimPlot3D | dimPlot3D |
| dimPlot_3D_plotly | dimPlot_3D_plotly |
| do_cell_proximity_test | do_cell_proximity_test |
| do_cell_proximity_test_spot | do_cell_proximity_test_spot |
| doHclust | doHclust |
| doHMRF | doHMRF |
| doHMRF_V2 | doHMRF_V2 |
| 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 |
| doSNNCluster | doSNNCluster |
| do_spatial_grid_averaging | do_spatial_grid_averaging |
| do_spatial_knn_smoothing | do_spatial_knn_smoothing |
| do_ttest | do_ttest |
| do_wilctest | do_wilctest |
| DT_removeNA | DT_removeNA |
| dt_to_matrix | dt_to_matrix |
| enrich_analysis | enrich_analysis |
| enrich_deconvolution | enrich_deconvolution |
| estimateCellCellDistance | estimateCellCellDistance |
| estimateImageBg | estimateImageBg |
| evaluate_expr_matrix | evaluate_expr_matrix |
| evaluate_spatial_locations | evaluate_spatial_locations |
| explainGiottoInstructions | explainGiottoInstructions |
| exportGiottoViewer | exportGiottoViewer |
| exprCellCellcom | exprCellCellcom |
| extended_gini_fun | extended_gini_fun |
| extend_vector | extend_vector |
| extractNearestNetwork | extractNearestNetwork |
| fDataDT | fDataDT |
| filterCellProximityGenes | filterCellProximityGenes |
| filterCombinations | filterCombinations |
| filterCPG | filterCPG |
| filterDistributions | filterDistributions |
| filterGiotto | filterGiotto |
| filterICG | filterICG |
| filterICGSpot | filterICGSpot |
| filterInteractionChangedGenes | filterInteractionChangedGenes |
| filter_network | filter_network |
| filterSpatialGenes | filterSpatialGenes |
| findCellProximityGenes | findCellProximityGenes |
| findCellProximityGenes_per_interaction | findCellProximityGenes_per_interaction |
| 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 |
| findICG | findICG |
| findICG_per_interaction_spot | findICG_per_interaction_spot |
| findICGSpot | findICGSpot |
| findInteractionChangedGenes | findInteractionChangedGenes |
| findMarkers | findMarkers |
| findMarkers_one_vs_all | findMarkers_one_vs_all |
| findMastMarkers | findMastMarkers |
| findMastMarkers_one_vs_all | findMastMarkers_one_vs_all |
| findNetworkNeighbors | findNetworkNeighbors |
| findScranMarkers | findScranMarkers |
| findScranMarkers_one_vs_all | findScranMarkers_one_vs_all |
| find_x_y_ranges | find_x_y_ranges |
| flex_lapply | flex_lapply |
| FSV_show | FSV_show |
| geneExpDWLS | geneExpDWLS |
| general_save_function | general_save_function |
| get10Xmatrix | get10Xmatrix |
| get10Xmatrix_h5 | get10Xmatrix_h5 |
| getClusterSimilarity | getClusterSimilarity |
| get_cross_section_coordinates | get_cross_section_coordinates |
| getDendrogramSplits | getDendrogramSplits |
| get_distance | get_distance |
| getDistinctColors | getDistinctColors |
| getGiottoImage | getGiottoImage |
| get_os | get_os |
| get_sectionThickness | get_sectionThickness |
| getSpatialDataset | getSpatialDataset |
| ggplot_save_function | ggplot_save_function |
| giotto-class | S4 giotto Class |
| giotto_lapply | giotto_lapply |
| heatmSpatialCorGenes | heatmSpatialCorGenes |
| hyperGeometricEnrich | hyperGeometricEnrich |
| initHMRF_V2 | initHMRF_V2 |
| insertCrossSectionGenePlot3D | insertCrossSectionGenePlot3D |
| insertCrossSectionSpatPlot3D | insertCrossSectionSpatPlot3D |
| install_giotto_environment | install_giotto_environment |
| installGiottoEnvironment | installGiottoEnvironment |
| install_giotto_environment_specific | install_giotto_environment_specific |
| jackstrawPlot | jackstrawPlot |
| join_expression | join_expression |
| 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 | libNorm_giotto |
| loadHMRF | loadHMRF |
| 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 |
| mean_giotto | mean_giotto |
| mergeClusters | mergeClusters |
| mini_giotto_3D | mini Giotto object for spatial single-cell 3D data |
| mini_giotto_multi_cell | mini Giotto object for spatial multi-cell resolution data |
| mini_giotto_single_cell | mini Giotto object for spatial single-cell resolution data |
| my_arowMeans | my_arowMeans |
| mygini_fun | mygini_fun |
| my_growMeans | my_growMeans |
| my_rowMeans | my_rowMeans |
| nnDT_to_kNN | nnDT_to_kNN |
| node_clusters | node_clusters |
| normalizeGiotto | normalizeGiotto |
| numPts_below_line | numPts_below_line |
| optimize_deconvolute_dwls | optimize_deconvolute_dwls |
| optimize_solveDampenedWLS | optimize_solveDampenedWLS |
| OR_test_fnc | OR_test_fnc |
| package_check | package_check |
| PAGE_DT_method | PAGE_DT_method |
| PAGEEnrich | PAGEEnrich |
| pca_giotto | pca_giotto |
| pDataDT | pDataDT |
| pipe | Pipe operator |
| plotCCcomDotplot | plotCCcomDotplot |
| plotCCcomHeatmap | plotCCcomHeatmap |
| plotCellProximityGenes | plotCellProximityGenes |
| plotCellProximityGenesSpot | plotCellProximityGenesSpot |
| plotCombineCCcom | plotCombineCCcom |
| plotCombineCellCellCommunication | plotCombineCellCellCommunication |
| plotCombineCellProximityGenes | plotCombineCellProximityGenes |
| plotCombineCPG | plotCombineCPG |
| plotCombineICG | plotCombineICG |
| plotCombineInteractionChangedGenes | plotCombineInteractionChangedGenes |
| plotCPG | plotCPG |
| plotGiottoImage | plotGiottoImage |
| plotHeatmap | plotHeatmap |
| plotICG | plotICG |
| plotICGSpot | plotICGSpot |
| plotInteractionChangedGenes | plotInteractionChangedGenes |
| 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_network_layer_ggplot | plot_network_layer_ggplot |
| plotPCA | plotPCA |
| plotPCA_2D | plotPCA_2D |
| plotPCA_3D | plotPCA_3D |
| plot_point_layer_ggplot | plot_point_layer_ggplot |
| plot_point_layer_ggplot_noFILL | plot_point_layer_ggplot_noFILL |
| plotRankSpatvsExpr | plotRankSpatvsExpr |
| plotRecovery | plotRecovery |
| plotRecovery_sub | plotRecovery_sub |
| plot_spat_image_layer_ggplot | plot_spat_image_layer_ggplot |
| plot_spat_point_layer_ggplot | plot_spat_point_layer_ggplot |
| plot_spat_point_layer_ggplot_noFILL | plot_spat_point_layer_ggplot_noFILL |
| plot_spat_scatterpie_layer_ggplot | plot_spat_scatterpie_layer_ggplot |
| plot_spat_voronoi_layer_ggplot | plot_spat_voronoi_layer_ggplot |
| plotStatDelaunayNetwork | plotStatDelaunayNetwork |
| plotTSNE | plotTSNE |
| plotTSNE_2D | plotTSNE_2D |
| plotTSNE_3D | plotTSNE_3D |
| plotUMAP | plotUMAP |
| plotUMAP_2D | plotUMAP_2D |
| plotUMAP_3D | plotUMAP_3D |
| processGiotto | processGiotto |
| projection_fun | projection_fun |
| rank_binarize | rank_binarize |
| rankEnrich | rankEnrich |
| rankSpatialCorGroups | rankSpatialCorGroups |
| read_crossSection | read_crossSection |
| readExprMatrix | readExprMatrix |
| readGiottoInstructions | readGiottoInstrunctions |
| register_spatial_locations | register_spatial_locations |
| removeCellAnnotation | removeCellAnnotation |
| removeGeneAnnotation | removeGeneAnnotation |
| removeGiottoEnvironment | removeGiottoEnvironment |
| replaceGiottoInstructions | replaceGiottoInstructions |
| 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 |
| rotate_spatial_locations | rotate_spatial_locations |
| rowMeans_flex | rowMeans_flex |
| rowMeans_giotto | rowMeans_giotto |
| rowSums_flex | rowSums_flex |
| rowSums_giotto | rowSums_giotto |
| runDWLSDeconv | runDWLSDeconv |
| runHyperGeometricEnrich | runHyperGeometricEnrich |
| runPAGEEnrich | runPAGEEnrich |
| runPAGEEnrich_OLD | runPAGEEnrich_OLD |
| runPatternSimulation | runPatternSimulation |
| runPCA | runPCA |
| runPCA_factominer | runPCA_factominer |
| runPCA_prcomp_irlba | runPCA_prcomp_irlba |
| runRankEnrich | runRankEnrich |
| 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 | runtSNE |
| runUMAP | runUMAP |
| sampling_sp_genes | sampling_sp_genes |
| scale_spatial_locations | scale_spatial_locations |
| screePlot | screePlot |
| select_dimReduction | select_dimReduction |
| select_expression_values | select_expression_values |
| select_NearestNetwork | select_NearestNetwork |
| selectPatternGenes | selectPatternGenes |
| select_spatialGrid | select_spatialGrid |
| select_spatialNetwork | select_spatialNetwork |
| set_giotto_python_path | set_giotto_python_path |
| showClusterDendrogram | showClusterDendrogram |
| showClusterHeatmap | showClusterHeatmap |
| showGiottoImageNames | showGiottoImageNames |
| showGiottoInstructions | showGiottoInstructions |
| showGrids | showGrids |
| show-methods | show method for giotto class |
| showNetworks | showNetworks |
| showPattern | showPattern |
| showPattern2D | showPattern2D |
| showPattern3D | showPattern3D |
| showPatternGenes | showPatternGenes |
| showProcessingSteps | showProcessingSteps |
| showSaveParameters | showSaveParameters |
| showSpatialCorGenes | showSpatialCorGenes |
| signPCA | signPCA |
| silhouetteRank | silhouetteRank |
| silhouetteRankTest | silhouetteRankTest |
| simulateOneGenePatternGiottoObject | simulateOneGenePatternGiottoObject |
| 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 |
| spatDeconvPlot | spatDeconvPlot |
| spatDimCellPlot | spatDimCellPlot |
| spatDimCellPlot2D | spatDimCellPlot2D |
| spatDimGenePlot | spatDimGenePlot |
| spatDimGenePlot2D | spatDimGenePlot2D |
| spatDimGenePlot3D | spatDimGenePlot3D |
| spatDimPlot | spatDimPlot |
| spatDimPlot2D | spatDimPlot2D |
| spatDimPlot3D | spatDimPlot3D |
| spat_fish_func | spat_fish_func |
| spat_fish_func_DT | spat_fish_func_DT |
| spatGenePlot | spatGenePlot |
| spatGenePlot2D | spatGenePlot2D |
| spatGenePlot3D | spatGenePlot3D |
| spatialAEH | spatialAEH |
| spatialDE | spatialDE |
| spatNetwDistributions | spatNetwDistributionsDistance |
| spatNetwDistributionsDistance | spatNetwDistributionsDistance |
| 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 |
| specific_CCCScores_spots | specific_CCCScores_spots |
| specificCellCellcommunicationScores | specificCellCellcommunicationScores |
| split_dendrogram_in_two | split_dendrogram_in_two |
| spot_deconvolution | spot_deconvolution |
| stack_spatlocs | stack_spatlocs |
| standardise_flex | standardise_flex |
| standardise_giotto | standardise_giotto |
| stitchFieldCoordinates | stitchFieldCoordinates |
| stitchTileCoordinates | stitchTileCoordinates |
| subClusterCells | subClusterCells |
| subsetGiotto | subsetGiotto |
| subsetGiottoLocs | subsetGiottoLocs |
| t_flex | t_flex |
| t_giotto | t_giotto |
| trakem2_rigid_transf_extract | trakem2_rigid_transf_extract |
| transform_2d_mesh_to_3d_mesh | transform_2d_mesh_to_3d_mesh |
| trendSceek | trendSceek |
| updateGiottoImage | updateGiottoImage |
| viewHMRFresults | viewHMRFresults |
| viewHMRFresults2D | viewHMRFresults2D |
| viewHMRFresults3D | viewHMRFresults3D |
| viewHMRFresults_V2 | viewHMRFresults_V2 |
| violinPlot | violinPlot |
| 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 |
| xy_translate_spatial_locations | xy_translate_spatial_locations |
