Man pages for sqjin/CellChat
Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data
| addMeta | Add the cell information into meta slot |
| aggregateNet | Calculate the aggregated network by counting the number of... |
| alpha_centrality | compute alpha centrality |
| AnyMatrix-class | The CellChat Class |
| barPlot | Bar plot for average gene expression |
| barplot_internal | Bar plot for dataframe |
| buildSNN | Build SNN matrix |
| CellChat-class | The key slots used in the CellChat object are described... |
| CellChatDB.human | Ligand-receptor interactions in CellChat database for human |
| CellChatDB.mouse | Ligand-receptor interactions in CellChat database for mouse |
| CellChatDB.zebrafish | Ligand-receptor interactions in CellChat database for... |
| CellChat_theme_opts | ggplot theme in CellChat |
| checkGeneSymbol | check the official Gene Symbol |
| colorRamp3 | Color interpolation |
| compareInteractions | Comparing the number of inferred communication links between... |
| computeAveExpr | Compute averaged expression values for each cell group |
| computeCentralityLocal | Compute Centrality measures for a signaling network |
| computeCommunProb | Compute the communication probability/strength between any... |
| computeCommunProbPathway | Compute the communication probability on signaling pathway... |
| computeEigengap | Compute the eigengap of a given matrix for inferring the... |
| computeEnrichmentScore | Compute and visualize the enrichment score of ligand-receptor... |
| computeExpr_agonist | Modeling the effect of agonist on the ligand-receptor... |
| computeExpr_antagonist | Modeling the effect of antagonist on the ligand-receptor... |
| computeExpr_complex | Compute the expression of complex in individual cells using... |
| computeExpr_coreceptor | Modeling the effect of coreceptor on the ligand-receptor... |
| computeExprGroup_agonist | Modeling the effect of agonist on the ligand-receptor... |
| computeExprGroup_antagonist | Modeling the effect of antagonist on the ligand-receptor... |
| computeExpr_LR | Compute the expression of ligands or receptors using... |
| computeLaplacian | Compute eigenvalues of associated Laplacian matrix of a given... |
| computeNetD_structure | Compute the structural distance between two signaling... |
| computeNetSimilarity | Compute signaling network similarity for any pair of... |
| computeNetSimilarityPairwise | Compute signaling network similarity for any pair of datasets |
| computeRegionDistance | Compute the region distance based on the spatial locations of... |
| createCellChat | Create a new CellChat object from a data matrix, Seurat or... |
| dotPlot | Dot plot |
| entropia | compute the Shannon entropy |
| extractEnrichedLR | Identify all the significant interactions (L-R pairs) and... |
| extractEnrichedLR_internal | Identify all the significant interactions (L-R pairs) and... |
| extractGene | Extract the genes involved in CellChatDB |
| extractGeneSubset | Extract the gene name |
| extractGeneSubsetFromPair | Extract the signaling gene names from ligand-receptor pairs |
| extract_max | extract the max value of the y axis |
| filterCommunication | Filter cell-cell communication if there are only few number... |
| geometricMean | Compute the geometric mean |
| getMaxWeight | Compute the maximum value of certain measures in the inferred... |
| ggPalette | Generate ggplot2 colors |
| identifyCommunicationPatterns | Identification of major signals for specific cell groups and... |
| identifyEnrichedInteractions | Identify all the significant interactions (L-R pairs) from... |
| identifyOverExpressedGenes | Identify over-expressed signaling genes associated with each... |
| identifyOverExpressedInteractions | Identify over-expressed ligand-receptor interactions (pairs)... |
| identifyOverExpressedLigandReceptor | Identify over-expressed ligands and (complex) receptors... |
| l1NormalizeColumns | Column-normalize a sparse, symmetric matrix (using the l1... |
| l1NormalizeRows | Row-normalize a sparse, symmetric matrix (using the l1 norm)... |
| liftCellChat | Update a CellChat object by lifting up the cell groups to the... |
| mergeCellChat | Merge CellChat objects |
| mergeInteractions | Compute the number of interactions/interaction strength... |
| modify_vlnplot | modified vlnplot |
| mycircle | generate circle symbol |
| netAnalysis_computeCentrality | Compute the network centrality scores allowing identification... |
| netAnalysis_contribution | Compute and visualize the contribution of each... |
| netAnalysis_diff_signalingRole_scatter | 2D visualization of differential signaling roles (dominant... |
| netAnalysis_dot | Dot plots showing the associations of latent patterns with... |
| netAnalysis_river | River plot showing the associations of latent patterns with... |
| netAnalysis_signalingChanges_scatter | 2D visualization of differential outgoing and incoming... |
| netAnalysis_signalingRole_heatmap | Heatmap showing the contribution of signals (signaling... |
| netAnalysis_signalingRole_network | Heatmap showing the centrality scores/importance of cell... |
| netAnalysis_signalingRole_scatter | 2D visualization of dominant senders (sources) and receivers... |
| netClustering | Classification learning of the signaling networks |
| netEmbedding | Manifold learning of the signaling networks based on their... |
| netMappingDEG | Mapping the differential expressed genes (DEG) information... |
| netVisual | Visualize the inferred cell-cell communication network |
| netVisual_aggregate | Visualize the inferred signaling network of signaling... |
| netVisual_barplot | Visualization of (differential) number of interactions |
| netVisual_bubble | Show all the significant interactions (L-R pairs) from some... |
| netVisual_chord_cell | Chord diagram for visualizing cell-cell communication for a... |
| netVisual_chord_cell_internal | Chord diagram for visualizing cell-cell communication from a... |
| netVisual_chord_gene | Chord diagram for visualizing cell-cell communication for a... |
| netVisual_circle | Circle plot of cell-cell communication network |
| netVisual_diffInteraction | Circle plot showing differential cell-cell communication... |
| netVisual_embedding | 2D visualization of the learned manifold of signaling... |
| netVisual_embeddingPairwise | 2D visualization of the joint manifold learning of signaling... |
| netVisual_embeddingPairwiseZoomIn | Zoom into the 2D visualization of the joint manifold learning... |
| netVisual_embeddingZoomIn | Zoom into the 2D visualization of the learned manifold... |
| netVisual_heatmap | Visualization of network using heatmap |
| netVisual_hierarchy1 | Hierarchy plot of cell-cell communications sending to cell... |
| netVisual_hierarchy2 | Hierarchy plot of cell-cell communication sending to cell... |
| netVisual_individual | Visualize the inferred signaling network of individual L-R... |
| netVisual_spatial | Spatial plot of cell-cell communication network |
| nnd | compute nnd |
| node_distance | compute the node distance matrix |
| normalizeData | Normalize data using a scaling factor |
| pieChart | Plot pie chart |
| plotGeneExpression | A Seurat wrapper function for plotting gene expression using... |
| PPI.human | Human Protein-Protein interactions |
| PPI.mouse | Mouse Protein-Protein interactions |
| projectAndRecombine | Perform network projecting on network when the network genes... |
| projectData | Project gene expression data onto a protein-protein... |
| projectFromNetworkRecombine | Combine gene expression from projected space (that of the... |
| projectOnNetwork | Project the gene expression matrix onto a lower space of the... |
| randomWalkBySolve | project data on graph by solving the linear equation (I -... |
| rankNet | Rank signaling networks based on the information flow or the... |
| rankNetPairwise | Rank ligand-receptor interactions for any pair of two cell... |
| rankSimilarity | Rank the similarity of the shared signaling pathways based on... |
| runPCA | Dimension reduction using PCA |
| runUMAP | Run UMAP |
| scaleData | Scale the data |
| scaleMat | Scale a data matrix |
| scPalette | Generate colors from a customed color palette |
| searchPair | Subset the ligand-receptor interactions for given specific... |
| selectK | Select the number of the patterns for running... |
| setIdent | Set the default identity of cells |
| show-CellChat-method | show method for CellChat |
| showDatabaseCategory | Show the description of CellChatDB databse |
| sketchData | Downsampling single cell data using geometric sketching... |
| spatialDimPlot | Visualize spatial cell groups |
| spatialFeaturePlot | A spatial feature plots |
| StackedVlnPlot | Stacked Violin plot |
| subsetCellChat | Subset CellChat object using a portion of cells |
| subsetCommunication | Subset the inferred cell-cell communications of interest |
| subsetCommunication_internal | Subset the inferred cell-cell communications of interest |
| subsetData | Subset the expression data of signaling genes for saving... |
| subsetDB | Subset CellChatDB databse by only including interactions of... |
| thresholdedMean | Compute the average expression per cell group when the... |
| triMean | Compute the Tukey's trimean |
| updateCellChat | Update a single CellChat object |
| updateClusterLabels | Update and re-order the cell group names after running... |
