| %>% |
Man page
|
| DT_removeNA |
Man page
Source code
|
| FSV_show |
Man page
|
| FUN |
Source code
|
| OR_test_fnc |
Man page
|
| PAGEEnrich |
Man page
|
| PAGE_DT_method |
Man page
Source code
|
| adapt_aspect_ratio |
Man page
Source code
|
| addCellIntMetadata |
Man page
|
| addCellMetadata |
Man page
|
| addCellStatistics |
Man page
|
| addGeneMetadata |
Man page
|
| addGeneStatistics |
Man page
|
| addGenesPerc |
Man page
|
| addGiottoImage |
Man page
|
| addGiottoImageToSpatPlot |
Man page
|
| addHMRF |
Man page
|
| addHMRF_V2 |
Man page
|
| addNetworkLayout |
Man page
|
| addStatistics |
Man page
|
| adjustGiottoMatrix |
Man page
|
| aes_string2 |
Man page
Source code
|
| all_plots_save_function |
Man page
Source code
|
| anndataToGiotto |
Man page
Source code
|
| annotateGiotto |
Man page
|
| annotateSpatialGrid |
Man page
|
| annotateSpatialNetwork |
Man page
Source code
|
| annotate_spatlocs_with_spatgrid_2D |
Man page
|
| annotate_spatlocs_with_spatgrid_3D |
Man page
|
| average_gene_gene_expression_in_groups |
Man page
|
| binSpect |
Man page
|
| binSpectMulti |
Man page
|
| binSpectSingle |
Man page
|
| cal_diff_per_interaction |
Man page
|
| cal_expr_residual |
Man page
|
| calc_spatial_enrichment_DT |
Man page
|
| calc_spatial_enrichment_matrix |
Man page
|
| calc_spatial_enrichment_minimum |
Man page
|
| calculateHVG |
Man page
Source code
|
| calculateMetaTable |
Man page
|
| calculateMetaTableCells |
Man page
|
| calculate_distance_and_weight |
Man page
Source code
|
| cellProximityBarplot |
Man page
Source code
|
| cellProximityEnrichment |
Man page
|
| cellProximityEnrichmentEachSpot |
Man page
|
| cellProximityEnrichmentSpots |
Man page
Source code
|
| cellProximityHeatmap |
Man page
Source code
|
| cellProximityNetwork |
Man page
Source code
|
| cellProximitySpatPlot |
Man page
Source code
|
| cellProximitySpatPlot2D |
Man page
Source code
|
| cellProximitySpatPlot3D |
Man page
Source code
|
| cellProximityVisPlot |
Man page
Source code
|
| cellProximityVisPlot_2D_ggplot |
Man page
Source code
|
| cellProximityVisPlot_2D_plotly |
Man page
Source code
|
| cellProximityVisPlot_3D_plotly |
Man page
Source code
|
| cell_proximity_spots |
Man page
Source code
|
| cell_proximity_spots_external |
Man page
Source code
|
| cell_proximity_spots_internal |
Man page
Source code
|
| changeGiottoInstructions |
Man page
Source code
|
| changeImageBg |
Man page
Source code
|
| checkAndFixSpatialGenes |
Man page
Source code
|
| checkGiottoEnvironment |
Man page
Source code
|
| chooseAvailableSpatialGenes |
Man page
Source code
|
| clusterCells |
Man page
|
| clusterSpatialCorGenes |
Man page
|
| cluster_enrich_analysis |
Man page
|
| colMeans_flex |
Man page
Source code
|
| colMeans_giotto |
Man page
Source code
|
| colSums_flex |
Man page
Source code
|
| colSums_giotto |
Man page
Source code
|
| combCCcom |
Man page
|
| combineCPG |
Man page
|
| combineCellProximityGenes |
Man page
|
| combineCellProximityGenes_per_interaction |
Man page
|
| combineICG |
Man page
|
| combineInteractionChangedGenes |
Man page
|
| combineMetadata |
Man page
|
| convertEnsemblToGeneSymbol |
Man page
Source code
|
| convert_mgImage_to_array_DT |
Man page
Source code
|
| convert_to_full_spatial_network |
Man page
Source code
|
| convert_to_reduced_spatial_network |
Man page
Source code
|
| cor_flex |
Man page
Source code
|
| cor_giotto |
Man page
Source code
|
| cor_sparse |
Man page
Source code
|
| createCrossSection |
Man page
Source code
|
| createGiottoImage |
Man page
|
| createGiottoInstructions |
Man page
Source code
|
| createGiottoObject |
Man page
Source code
|
| createGiottoVisiumObject |
Man page
Source code
|
| createHeatmap_DT |
Man page
Source code
|
| createMetagenes |
Man page
|
| createNearestNetwork |
Man page
Source code
|
| createRegZStackGobject |
Man page
Source code
|
| createSpatialDefaultGrid |
Man page
|
| createSpatialDelaunayNetwork |
Man page
Source code
|
| createSpatialEnrich |
Man page
|
| createSpatialGrid |
Man page
|
| createSpatialKNNnetwork |
Man page
|
| createSpatialNetwork |
Man page
Source code
|
| create_2d_mesh_grid_line_obj |
Man page
Source code
|
| create_KNNnetwork_dbscan |
Man page
Source code
|
| create_average_DT |
Man page
Source code
|
| create_average_detection_DT |
Man page
Source code
|
| create_cell_type_random_cell_IDs |
Man page
|
| create_cluster_matrix |
Man page
|
| create_crossSection_object |
Man page
Source code
|
| create_delaunayNetwork2D |
Man page
|
| create_delaunayNetwork3D |
Man page
|
| create_delaunayNetwork_RTriangle |
Man page
Source code
|
| create_delaunayNetwork_deldir |
Man page
Source code
|
| create_delaunayNetwork_geometry |
Man page
Source code
|
| create_delaunayNetwork_geometry_3D |
Man page
Source code
|
| create_dimObject |
Man page
Source code
|
| create_genes_to_use_matrix |
Man page
Source code
|
| create_jackstrawplot |
Man page
Source code
|
| create_mesh_grid_lines |
Man page
Source code
|
| create_screeplot |
Man page
Source code
|
| create_spatialGridObject |
Man page
|
| create_spatialGrid_default_2D |
Man page
|
| create_spatialGrid_default_3D |
Man page
|
| create_spatialNetworkObject |
Man page
Source code
|
| crossSectionGenePlot |
Man page
Source code
|
| crossSectionGenePlot3D |
Man page
Source code
|
| crossSectionPlot |
Man page
Source code
|
| crossSectionPlot3D |
Man page
Source code
|
| decide_cluster_order |
Man page
Source code
|
| detectSpatialCorGenes |
Man page
|
| detectSpatialPatterns |
Man page
|
| determine_cores |
Man page
Source code
|
| dimCellPlot |
Man page
|
| dimCellPlot2D |
Man page
|
| dimGenePlot |
Man page
|
| dimGenePlot2D |
Man page
|
| dimGenePlot3D |
Man page
|
| dimPlot |
Man page
|
| dimPlot2D |
Man page
|
| dimPlot2D_single |
Man page
|
| dimPlot3D |
Man page
|
| dimPlot_2D_plotly |
Man page
|
| dimPlot_3D_plotly |
Man page
|
| doHMRF |
Man page
|
| doHMRF_V2 |
Man page
|
| doHclust |
Man page
|
| doKmeans |
Man page
|
| doLeidenCluster |
Man page
Source code
|
| doLeidenSubCluster |
Man page
|
| doLouvainCluster |
Man page
Source code
|
| doLouvainCluster_community |
Man page
Source code
|
| doLouvainCluster_multinet |
Man page
Source code
|
| doLouvainSubCluster |
Man page
|
| doLouvainSubCluster_community |
Man page
|
| doLouvainSubCluster_multinet |
Man page
|
| doRandomWalkCluster |
Man page
Source code
|
| doSNNCluster |
Man page
Source code
|
| do_cell_proximity_test |
Man page
|
| do_cell_proximity_test_spot |
Man page
|
| do_limmatest |
Man page
|
| do_multi_permuttest_random |
Man page
|
| do_multi_permuttest_random_spot |
Man page
|
| do_page_permutation |
Man page
Source code
|
| do_permuttest |
Man page
|
| do_permuttest_original |
Man page
|
| do_permuttest_original_spot |
Man page
|
| do_permuttest_random |
Man page
|
| do_permuttest_random_spot |
Man page
|
| do_permuttest_spot |
Man page
|
| do_rank_permutation |
Man page
|
| do_spatial_grid_averaging |
Man page
|
| do_spatial_knn_smoothing |
Man page
|
| do_ttest |
Man page
|
| do_wilctest |
Man page
|
| dt_to_matrix |
Man page
Source code
|
| enrich_analysis |
Man page
|
| enrich_deconvolution |
Man page
|
| estimateCellCellDistance |
Man page
Source code
|
| estimateImageBg |
Man page
Source code
|
| evaluate_expr_matrix |
Man page
Source code
|
| evaluate_spatial_locations |
Man page
Source code
|
| explainGiottoInstructions |
Man page
Source code
|
| exportGiottoViewer |
Man page
Source code
|
| exprCellCellcom |
Man page
|
| extend_vector |
Man page
Source code
|
| extended_gini_fun |
Man page
Source code
|
| extractNearestNetwork |
Man page
|
| fDataDT |
Man page
Source code
|
| filterCPG |
Man page
|
| filterCellProximityGenes |
Man page
|
| filterCombinations |
Man page
Source code
|
| filterDistributions |
Man page
Source code
|
| filterGiotto |
Man page
|
| filterICG |
Man page
|
| filterICGSpot |
Man page
|
| filterInteractionChangedGenes |
Man page
|
| filterSpatialGenes |
Man page
Source code
|
| filter_network |
Man page
Source code
|
| findCPG |
Man page
|
| findCellProximityGenes |
Man page
|
| findCellProximityGenes_per_interaction |
Man page
|
| findGiniMarkers |
Man page
Source code
|
| findGiniMarkers_one_vs_all |
Man page
|
| findICG |
Man page
|
| findICGSpot |
Man page
|
| findICG_per_interaction_spot |
Man page
|
| findInteractionChangedGenes |
Man page
|
| findMarkers |
Man page
|
| findMarkers_one_vs_all |
Man page
|
| findMastMarkers |
Man page
|
| findMastMarkers_one_vs_all |
Man page
|
| findNetworkNeighbors |
Man page
|
| findScranMarkers |
Man page
Source code
|
| findScranMarkers_one_vs_all |
Man page
Source code
|
| find_dampening_constant |
Man page
|
| find_grid_2D |
Man page
Source code
|
| find_grid_3D |
Man page
Source code
|
| find_grid_x |
Man page
Source code
|
| find_grid_y |
Man page
|
| find_grid_z |
Man page
|
| find_x_y_ranges |
Man page
Source code
|
| flex_lapply |
Man page
Source code
|
| fun |
Source code
|
| geneExpDWLS |
Man page
|
| general_save_function |
Man page
Source code
|
| get10Xmatrix |
Man page
Source code
|
| get10Xmatrix_h5 |
Man page
Source code
|
| getClusterSimilarity |
Man page
|
| getDendrogramSplits |
Man page
|
| getDistinctColors |
Man page
Source code
|
| getGiottoImage |
Man page
|
| getSpatialDataset |
Man page
Source code
|
| get_cross_section_coordinates |
Man page
Source code
|
| get_distance |
Man page
Source code
|
| get_os |
Man page
Source code
|
| get_sectionThickness |
Man page
Source code
|
| ggplot_save_function |
Man page
Source code
|
| giotto |
Man page
|
| giotto-class |
Man page
|
| giotto_lapply |
Man page
Source code
|
| heatmSpatialCorGenes |
Man page
|
| hyperGeometricEnrich |
Man page
|
| initHMRF_V2 |
Man page
Source code
|
| insertCrossSectionGenePlot3D |
Man page
Source code
|
| insertCrossSectionSpatPlot3D |
Man page
Source code
|
| installGiottoEnvironment |
Man page
Source code
|
| install_giotto_environment |
Man page
Source code
|
| install_giotto_environment_specific |
Man page
Source code
|
| jackstrawPlot |
Man page
Source code
|
| join_expression |
Man page
Source code
|
| kmeans_arma_binarize |
Man page
Source code
|
| kmeans_arma_subset_binarize |
Man page
Source code
|
| kmeans_binarize |
Man page
Source code
|
| kmeans_binarize_wrapper |
Man page
Source code
|
| lapply_flex |
Man page
Source code
|
| libNorm_giotto |
Man page
Source code
|
| loadHMRF |
Man page
|
| logNorm_giotto |
Man page
Source code
|
| makeSignMatrixDWLS |
Man page
Source code
|
| makeSignMatrixDWLSfromMatrix |
Man page
Source code
|
| makeSignMatrixPAGE |
Man page
Source code
|
| makeSignMatrixRank |
Man page
Source code
|
| make_simulated_network |
Man page
Source code
|
| mean_expr_det_test |
Man page
Source code
|
| mean_flex |
Man page
Source code
|
| mean_giotto |
Man page
Source code
|
| mergeClusters |
Man page
|
| mini_giotto_3D |
Man page
|
| mini_giotto_multi_cell |
Man page
|
| mini_giotto_single_cell |
Man page
|
| my_arowMeans |
Man page
Source code
Source code
|
| my_growMeans |
Man page
Source code
Source code
|
| my_rowMeans |
Man page
Source code
Source code
|
| mygini_fun |
Man page
Source code
|
| nnDT_to_kNN |
Man page
|
| node_clusters |
Man page
|
| normalizeGiotto |
Man page
|
| numPts_below_line |
Man page
Source code
|
| optimize_deconvolute_dwls |
Man page
|
| optimize_solveDampenedWLS |
Man page
|
| pDataDT |
Man page
Source code
|
| package_check |
Man page
Source code
|
| pca_giotto |
Man page
Source code
|
| plotCCcomDotplot |
Man page
Source code
|
| plotCCcomHeatmap |
Man page
Source code
|
| plotCPG |
Man page
Source code
|
| plotCellProximityGenes |
Man page
Source code
|
| plotCellProximityGenesSpot |
Man page
|
| plotCombineCCcom |
Man page
Source code
|
| plotCombineCPG |
Man page
Source code
|
| plotCombineCellCellCommunication |
Man page
Source code
|
| plotCombineCellProximityGenes |
Man page
Source code
|
| plotCombineICG |
Man page
Source code
|
| plotCombineInteractionChangedGenes |
Man page
Source code
|
| plotGiottoImage |
Man page
|
| plotHeatmap |
Man page
Source code
|
| plotICG |
Man page
Source code
|
| plotICGSpot |
Man page
|
| plotInteractionChangedGenes |
Man page
Source code
|
| plotMetaDataCellsHeatmap |
Man page
Source code
|
| plotMetaDataHeatmap |
Man page
Source code
|
| plotPCA |
Man page
|
| plotPCA_2D |
Man page
|
| plotPCA_3D |
Man page
|
| plotRankSpatvsExpr |
Man page
Source code
|
| plotRecovery |
Man page
Source code
|
| plotRecovery_sub |
Man page
Source code
|
| plotStatDelaunayNetwork |
Man page
Source code
|
| plotTSNE |
Man page
|
| plotTSNE_2D |
Man page
|
| plotTSNE_3D |
Man page
|
| plotUMAP |
Man page
|
| plotUMAP_2D |
Man page
|
| plotUMAP_3D |
Man page
|
| plot_network_layer_ggplot |
Man page
Source code
|
| plot_point_layer_ggplot |
Man page
Source code
|
| plot_point_layer_ggplot_noFILL |
Man page
|
| plot_spat_image_layer_ggplot |
Man page
|
| plot_spat_point_layer_ggplot |
Man page
|
| plot_spat_point_layer_ggplot_noFILL |
Man page
|
| plot_spat_scatterpie_layer_ggplot |
Man page
|
| plot_spat_voronoi_layer_ggplot |
Man page
|
| plotly_axis_scale_2D |
Man page
Source code
|
| plotly_axis_scale_3D |
Man page
Source code
|
| plotly_grid |
Man page
Source code
|
| plotly_network |
Man page
Source code
|
| processGiotto |
Man page
|
| projection_fun |
Man page
Source code
|
| rankEnrich |
Man page
|
| rankSpatialCorGroups |
Man page
|
| rank_binarize |
Man page
Source code
|
| readExprMatrix |
Man page
Source code
|
| readGiottoInstructions |
Man page
Source code
|
| read_crossSection |
Man page
Source code
|
| register_spatial_locations |
Man page
Source code
|
| removeCellAnnotation |
Man page
|
| removeGeneAnnotation |
Man page
|
| removeGiottoEnvironment |
Man page
Source code
|
| replaceGiottoInstructions |
Man page
Source code
|
| reshape_to_data_point |
Man page
Source code
|
| reshape_to_mesh_grid_obj |
Man page
Source code
|
| return_giotto_environment_path |
Man page
Source code
|
| return_giotto_environment_path_executable |
Man page
Source code
|
| rotate_spatial_locations |
Man page
Source code
|
| rowMeans_flex |
Man page
Source code
|
| rowMeans_giotto |
Man page
Source code
|
| rowSums_flex |
Man page
Source code
|
| rowSums_giotto |
Man page
Source code
|
| runDWLSDeconv |
Man page
|
| runHyperGeometricEnrich |
Man page
|
| runPAGEEnrich |
Man page
|
| runPAGEEnrich_OLD |
Man page
Source code
|
| runPCA |
Man page
Source code
|
| runPCA_factominer |
Man page
Source code
|
| runPCA_prcomp_irlba |
Man page
Source code
|
| runPatternSimulation |
Man page
|
| runRankEnrich |
Man page
|
| runSpatialDeconv |
Man page
|
| runSpatialEnrich |
Man page
|
| runUMAP |
Man page
Source code
|
| run_spatial_sim_tests_multi |
Man page
|
| run_spatial_sim_tests_one_rep |
Man page
|
| runtSNE |
Man page
Source code
|
| sampling_sp_genes |
Man page
Source code
|
| scale_spatial_locations |
Man page
Source code
|
| screePlot |
Man page
Source code
|
| selectPatternGenes |
Man page
|
| select_NearestNetwork |
Man page
|
| select_dimReduction |
Man page
Source code
|
| select_expression_values |
Man page
Source code
|
| select_spatialGrid |
Man page
|
| select_spatialNetwork |
Man page
Source code
|
| set_giotto_python_path |
Man page
Source code
Source code
|
| show,giotto-method |
Man page
|
| showClusterDendrogram |
Man page
Source code
|
| showClusterHeatmap |
Man page
Source code
|
| showGiottoImageNames |
Man page
|
| showGiottoInstructions |
Man page
Source code
|
| showGrids |
Man page
|
| showNetworks |
Man page
Source code
|
| showPattern |
Man page
|
| showPattern2D |
Man page
|
| showPattern3D |
Man page
|
| showPatternGenes |
Man page
|
| showProcessingSteps |
Man page
|
| showSaveParameters |
Man page
Source code
|
| showSpatialCorGenes |
Man page
|
| signPCA |
Man page
Source code
|
| silhouetteRank |
Man page
|
| silhouetteRankTest |
Man page
|
| simulateOneGenePatternGiottoObject |
Man page
|
| solve_OLS_internal |
Man page
|
| solve_dampened_WLSj |
Man page
|
| sort_combine_two_DT_columns |
Man page
Source code
|
| spark |
Man page
|
| spatCellCellcom |
Man page
|
| spatCellCellcomSpots |
Man page
|
| spatCellPlot |
Man page
|
| spatCellPlot2D |
Man page
|
| spatDeconvPlot |
Man page
|
| spatDimCellPlot |
Man page
|
| spatDimCellPlot2D |
Man page
|
| spatDimGenePlot |
Man page
|
| spatDimGenePlot2D |
Man page
|
| spatDimGenePlot3D |
Man page
|
| spatDimPlot |
Man page
|
| spatDimPlot2D |
Man page
|
| spatDimPlot3D |
Man page
|
| spatGenePlot |
Man page
|
| spatGenePlot2D |
Man page
|
| spatGenePlot3D |
Man page
|
| spatNetwDistributions |
Man page
Source code
|
| spatNetwDistributionsDistance |
Man page
Source code
|
| spatNetwDistributionsKneighbors |
Man page
Source code
|
| spatPlot |
Man page
|
| spatPlot2D |
Man page
|
| spatPlot2D_single |
Man page
|
| spatPlot3D |
Man page
|
| spatPlot_2D_plotly |
Man page
|
| spatPlot_3D_plotly |
Man page
|
| spat_OR_func |
Man page
|
| spat_OR_func_DT |
Man page
|
| spat_fish_func |
Man page
Source code
|
| spat_fish_func_DT |
Man page
Source code
|
| spatialAEH |
Man page
|
| spatialDE |
Man page
|
| specificCellCellcommunicationScores |
Man page
|
| specific_CCCScores_spots |
Man page
|
| split_dendrogram_in_two |
Man page
|
| spot_deconvolution |
Man page
|
| stack_spatlocs |
Man page
Source code
|
| standardise_flex |
Man page
|
| standardise_giotto |
Man page
|
| stitchFieldCoordinates |
Man page
Source code
|
| stitchTileCoordinates |
Man page
|
| subClusterCells |
Man page
|
| subsetGiotto |
Man page
Source code
|
| subsetGiottoLocs |
Man page
Source code
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| t_flex |
Man page
Source code
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| t_giotto |
Man page
Source code
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| trakem2_rigid_transf_extract |
Man page
Source code
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| transform_2d_mesh_to_3d_mesh |
Man page
Source code
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| trendSceek |
Man page
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| updateGiottoImage |
Man page
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| viewHMRFresults |
Man page
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| viewHMRFresults2D |
Man page
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| viewHMRFresults3D |
Man page
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| viewHMRFresults_V2 |
Man page
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| violinPlot |
Man page
Source code
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| writeHMRFresults |
Man page
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| write_giotto_viewer_annotation |
Man page
Source code
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| write_giotto_viewer_dim_reduction |
Man page
Source code
|
| write_giotto_viewer_numeric_annotation |
Man page
Source code
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| xy_translate_spatial_locations |
Man page
Source code
|
