| circosPlot | To present a circos plot |
| cluster.lr.inten | To get interaction intensity between clusters and receptors |
| CommPath-class | To define the CommPath object and the key slots |
| CommPathData | Ligand-receptor pairs and pathway annotations in CommPath... |
| compareMarker | To conduct defferential expression test in select.ident... |
| comparePath | To conduct defferential activation test in select.ident... |
| createCommPath | To create a CommPath object |
| diffAllPath | To find differentially activated pathways in each identity... |
| diffPath | To find different enriched pathway between two group cells |
| dotPlot.LR | To present a dot plot for specific ligand-receptor pairs in... |
| dotPlot.pathway | To present a dot plot for top ligand-receptor pairs involved... |
| extract.info | To extract information from ident.path.dat |
| factor.to.character | To convert the variables in a data.frame from factor to... |
| filterLR | To screen LR pairs involved in activated pathways |
| filterLR.path.contain.lig | To retrieve activated pathways containing the ligand |
| filterLR.path.contain.rep | To screen LR pairs with receptors involved in activated... |
| filterPath | To remove those pathways containing only ligands which do not... |
| findLigand | To find the upstream identity classes and ligands of specific... |
| findLRmarker | To identify marker ligands and marker receptors in the... |
| findLRpairs | To find marker ligands and marker receptors |
| findLRpath | To find those pathways in which the genesets show overlap... |
| findReceptor | To find the downstream identity class of specific ligand... |
| getPathAttr | To retrieve the available statistical measures for pathways |
| LRcolor | To get the color for the dots representing receptors and... |
| LRinten.to.width | To transform LR intensity to line width |
| order.and.top | To extract top n element |
| orderCheck | To check whether the specified order of idents by users... |
| pasteIdent | To paste a vector of idents into a ',' separated string |
| pathChainPlot | To present the interactions for a selected cluster, including... |
| pathChainPlot.compare | To compare the pathway mediated cell-cell communication flow... |
| pathHeatmap | To plot a heatmap of those differentially enriched pathways... |
| pathNet | To integrate the statistics of LR interactions and associated... |
| pathNet.lig.path.stat | To integrate the statistics of LR interactions and the... |
| pathNetPlot | To present a net plot for pathways and upstream or downstream... |
| pathNetPlot.downstream | To present a net plot for pathways and downstream associated... |
| pathNetPlot.upstream | To present a net plot for pathways and upstream associated LR... |
| pathNet.rep.path.stat | To integrate the statistics of LR interactions and the... |
| pathPlot | To present the interactions for a selected cluster, including... |
| pathPlot.compare | To compare differentially activated pathways and the involved... |
| pathTest | Differential enrichment analysis by t.test or wilcox.txt |
| p.remove.inf | To adjust those p values==0 |
| rotated.axis.element.text | To set up the hjust and vjust of text on axises |
| scale_1 | To scale x with minimum equal to 1 and maximum equal to 2 |
| scorePath | To find different enriched pathway between two group cells |
| show-CommPath-method | Show method for CommPath |
| subsetCommPath | To subset a CommPath object |
| subsetMatrix | To subset a matrix while keeping the dimension |
