Man pages for RubD/Giotto
Spatial single-cell transcriptomics pipeline.

addCellMetadataaddCellMetadata
addCellStatisticsaddCellStatistics
addGeneMetadataaddGeneMetadata
addGeneStatisticsaddGeneStatistics
addHMRFaddHMRF
addNetworkLayoutaddNetworkLayout
addStatisticsaddStatistics
adjustGiottoMatrixadjustGiottoMatrix
allCellCellcommunicationsScoresallCellCellcommunicationsScores
annotateGiottoannotateGiotto
annotateSpatialNetworkannotateSpatialNetwork
annotate_spatlocs_with_spatgrid_2Dannotate_spatlocs_with_spatgrid_2D
annotate_spatlocs_with_spatgrid_3Dannotate_spatlocs_with_spatgrid_3D
average_gene_gene_expression_in_groupsaverage_gene_gene_expression_in_groups
binGetSpatialGenesbinGetSpatialGenes
calculateHVGcalculateHVG
calculateMetaTablecalculateMetaTable
calculateSpatialGenescalculateSpatialGenes
calculate_spatial_genes_pythoncalculate_spatial_genes_python
cellProximityBarplotcellProximityBarplot
cellProximityEnrichmentcellProximityEnrichment
cellProximityHeatmapcellProximityHeatmap
cellProximityNetworkcellProximityNetwork
cellProximityVisPlotcellProximityVisPlot
cellProximityVisPlot_2D_ggplotcellProximityVisPlot_2D_ggplot
cellProximityVisPlot_2D_plotlycellProximityVisPlot_2D_plotly
cellProximityVisPlot_3D_plotlycellProximityVisPlot_3D_plotly
clusterCellsclusterCells
create_average_detection_DTcreate_average_detection_DT
create_average_DTcreate_average_DT
create_cell_type_random_cell_IDscreate_cell_type_random_cell_IDs
create_cluster_matrixcreate_cluster_matrix
create_dimObjectcreate_dimObject
createGiottoObjectcreate Giotto object
createHeatmap_DTcreateHeatmap_DT
createNearestNetworkcreateNearestNetwork
createSpatialGridcreateSpatialGrid2
createSpatialGrid_2DcreateSpatialGrid_2D
createSpatialGrid_3DcreateSpatialGrid_3D
createSpatialNetworkcreateSpatialNetwork
decide_cluster_orderdecide_cluster_order
detectSpatialPatternsdetectSpatialPatterns
direction_test_CPGdirection_test_CPG
doHclustdoHclust
doHMRFdoHMRF
doKmeansdoKmeans
doLeidenClusterdoLeidenCluster
doLeidenSubClusterdoLeidenSubCluster
doLouvainClusterdoLouvainCluster
doLouvainCluster_communitydoLouvainCluster_community
doLouvainCluster_multinetdoLouvainCluster_multinet
doLouvainSubClusterdoLouvainSubCluster
doLouvainSubCluster_communitydoLouvainSubCluster_community
doLouvainSubCluster_multinetdoLouvainSubCluster_multinet
doRandomWalkClusterdoRandomWalkCluster
doSNNClusterdoSNNCluster
dt_to_matrixdt_to_matrix
exportGiottoViewerexportGiottoViewer
exprOnlyCellCellcommunicationScoresexprOnlyCellCellcommunicationScores
extended_gini_funextended_gini_fun
extractNearestNetworkextractNearestNetwork
fDataDTfDataDT
filterCombinationsfilterCombinations
filterDistributionsfilterDistributions
filterGiottofilterGiotto
findGiniMarkersfindGiniMarkers
findGiniMarkers_one_vs_allfindGiniMarkers_one_vs_all
find_grid_2Dfind_grid_2D
find_grid_3Dfind_grid_3D
find_grid_xfind_grid_x
find_grid_yfind_grid_y
find_grid_zfind_grid_z
findMarkersfindMarkers
findMarkers_one_vs_allfindMarkers_one_vs_all
findMastMarkersfindMastMarkers
findMastMarkers_one_vs_allfindMastMarkers_one_vs_all
findScranMarkersfindScranMarkers
findScranMarkers_one_vs_allfindScranMarkers_one_vs_all
fish_functionfish_function
fish_function2fish_function2
FSV_showFSV_show
GenePattern_showGenePattern_show
getCellProximityGeneScoresgetCellProximityGeneScores
get_cell_to_cell_sorted_name_conversionget_cell_to_cell_sorted_name_conversion
getClusterSimilaritygetClusterSimilarity
getDendrogramSplitsgetDendrogramSplits
getDistinctColorsgetDistinctColors
getGeneToGeneSelectiongetGeneToGeneSelection
get_interaction_gene_enrichmentget_interaction_gene_enrichment
get_specific_interaction_gene_enrichmentget_specific_interaction_gene_enrichment
giotto-classS4 giotto Class
iterClusteriterCluster
iterLeidenClusteriterLeidenCluster
iterLouvainClusteriterLouvainCluster
iterLouvainCluster_communityiterLouvainCluster_community
iterLouvainCluster_multinetiterLouvainCluster_multinet
kmeans_binarizekmeans_binarize
loadHMRFloadHMRF
make_simulated_networkmake_simulated_network
mergeClustersmergeClusters
mygini_funmygini_fun
nnDT_to_kNNnnDT_to_kNN
node_clustersnode_clusters
normalizeGiottonormalizeGiotto
OR_function2OR_function2
pDataDTpDataDT
pipePipe operator
plotCPGscoresplotCPGscores
plotGTGscoresplotGTGscores
plotHeatmapplotHeatmap
plotly_axis_scale_2Dplotly_axis_scale_2D
plotly_axis_scale_3Dplotly_axis_scale_3D
plotly_gridplotly_grid
plotly_networkplotly_network
plotMetaDataHeatmapplotMetaDataHeatmap
plot_network_layer_ggplotplot_network_layer_ggplot
plotPCAplotPCA
plot_point_layer_ggplotplot_point_layer_ggplot
plotTSNEplotTSNE
plotUMAPplotUMAP
print.giottoprint method for giotto class
rank_binarizerank_binarize
runPCArunPCA
runtSNEruntSNE
runUMAPrunUMAP
select_expression_valuesselect_expression_values
selectPatternGenesselectPatternGenes
showClusterDendrogramshowClusterDendrogram
showClusterHeatmapshowClusterHeatmap
showCPGscoresshowCPGscores
showGeneExpressionProximityScoreshowGeneExpressionProximityScore
show-giotto-methodshow method for giotto class
showGTGscoresshowGTGscores
showIntExpressionProximityScoreshowIntExpressionProximityScore
showPatternshowPattern
showPatternGenesshowPatternGenes
showProcessingStepsshowProcessingSteps
showTopGeneToGeneshowTopGeneToGene
signPCAsignPCA
Spatial_AEHSpatial_AEH
Spatial_DESpatial_DE
specificCellCellcommunicationScoresspecificCellCellcommunicationScores
split_dendrogram_in_twosplit_dendrogram_in_two
stitchFieldCoordinatesstitchFieldCoordinates
subClusterCellssubClusterCells
subsetGiottosubsetGiotto
viewHMRFresultsviewHMRFresults
violinPlotviolinPlot
visDimGenePlotvisDimGenePlot
visDimGenePlot_2D_ggplotvisDimGenePlot_2D_ggplot
visDimGenePlot_3D_plotlyvisDimGenePlot_3D_plotly
visDimPlotvisDimPlot
visDimPlot_2D_ggplotvisDimPlot_2D_ggplot
visDimPlot_2D_plotlyvisDimPlot_2D_plotly
visDimPlot_3D_plotlyvisDimPlot_3D_plotly
visForceLayoutPlotvisForceLayoutPlot
visGenePlotvisGenePlot
visGenePlot_2D_ggplotvisGenePlot_2D_ggplot
visGenePlot_3D_plotlyvisGenePlot_3D_plotly
visPlotvisPlot
visPlot_2D_ggplotvisPlot_2D_ggplot
visPlot_2D_plotlyvisPlot_2D_plotly
visPlot_3D_plotlyvisPlot_3D_plotly
visSpatDimGenePlotvisSpatDimGenePlot
visSpatDimGenePlot_2DvisSpatDimGenePlot_2D
visSpatDimGenePlot_3DvisSpatDimGenePlot_3D
visSpatDimPlotvisSpatDimPlot
visSpatDimPlot_2DvisSpatDimPlot_2D
visSpatDimPlot_3DvisSpatDimPlot_3D
write_giotto_viewer_annotationwrite_giotto_viewer_annotation
write_giotto_viewer_dim_reductionwrite_giotto_viewer_dim_reduction
RubD/Giotto documentation built on Nov. 7, 2019, 5:36 a.m.