Man pages for martaint/InterCellar
InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
| annotateGO | Perform GO annotation of input data |
| annotatePathways | Annotate pathways for input data |
| buildPairsbyFunctionMatrix | Build binary matrix with int-pairs in rows, functions in cols |
| checkLL_RR | Manually change the annotation of L-L and R-R pairs |
| circlePlot | Plot circle plot |
| combineAnnotations | Combine GO annotation and pathways in a unique object |
| createBarPlot1_ggplot | Create ggplot barplot to be saved in tiff |
| createBarPlot2_CV | Create barplot of number of interaction for selected cluster |
| createBarPlot2_ggplot | Create ggplot barplot of Nint per cluster selected |
| createBarPlot_CV | Create Barplot cluster-verse |
| createNetwork | Create Network of clusters |
| dendroIntPairModules | Get dendrogram of int pair modules |
| elbowPoint | Determine the elbow point on a curve (from package akmedoids) |
| ensemblLink | Get html link to ensembl |
| getBack2BackBarplot | Get back-to-back barplot for 2 conditions comparison |
| getBarplotDF | Get dataframe for plotting barplot (all clusters) |
| getBarplotDF2 | Get dataframe for barplot (by cluster) |
| getClusterA_Names | Get cluster names only from sender cluster A |
| getClusterColors | Get colors for clusters |
| getClusterNames | Get clusters names from initial input data |
| getClusterNetwork | Creating edges dataframe for network of clusters |
| getClusterSize | Get Clusters size |
| getDistinctCouplets | Get table of unique int-pairs/clust-pairs couplets |
| getDotPlot_selInt | Functions to plot DotPlots |
| getGeneTable | Get table for gene-verse |
| getGObiomaRt | Connection to Ensembl via biomaRt to get GO terms |
| getHitsf | Subfunction to calculate significant functions by permutation... |
| getIntFlow | Get subset of interactions corresponding to a certain... |
| getNtermsBYdb | Calculate number of terms of a database |
| getNumLR | Get number of unique ligands and receptors |
| getPieChart | Get Pie Chart of unique couplets |
| getRadar_df | #' Get radar plot of relative numbers of interactions for a... |
| getRankedTerms | Get table with ranked functional terms |
| getSignificantFunctions | Calculate significant function per intpair module |
| getSignificantFunctions_multiCond | Get significance of functional terms related to unique... |
| getSignif_table | Wrapper for other functions to get significant table of func... |
| getSunburst | Get Sunburst plot of selected functional terms |
| getUMAPipModules | Get UMAP for IP modules |
| getUniqueDotplot | Plot dotplot containing only unique int-pair/cluster pairs... |
| getUniqueIntpairs_byCond | Get table of unique int-pairs by condition |
| goLink | Get GO link |
| input.data | Input Data example |
| read.cellchat | Read dataframe of cell-cell communication from CellChat... |
| read.CPDBv2 | Read output from CellPhoneDB v2. |
| read.customInput | Read custom input file and re-structure it with InterCellar... |
| read.icellnet | Read ICELLNET dataframe |
| read.SCsignalR | Read output from SingleCellSignalR |
| run_app | Run the Shiny Application |
| subsetAnnot_multiCond | Subset int-pair by function matrices to unique int-pairs by... |
| subsetFuncMatBYFlow | Subset pairs-function matrix by selected flow |
| swap.RLint | Swaps interaction pairs that are R-L to L-R |
| uniprotLink | Get html link to uniprot |
| updateInputLR | Function that orders all interaction pairs as L-R. Leaves... |
