# InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

## Documentation for package ‘InterCellar’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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)
getClusterNames | Get clusters names from initial input data
getClusterNetwork | Creating edges dataframe for network of clusters
getClusterSize | Get Clusters size
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 test
getIntFlow | Get subset of interactions corresponding to a certain viewpoint and flow
getNtermsBYdb | Calculate number of terms of a database
getNumLR | Get number of unique ligands and receptors
getRadarPlot | Get radar plot of relative numbers of interactions for a certain cell type
getRankedTerms | Get table with ranked functional terms
getSignificantFunctions | Calculate significant function per intpair module
getSunburst | Get Sunburst plot of selected functional terms
getUMAPipModules | Get UMAP for IP modules
getUniqueDotplot | Plot dotplot containing only unique int-pair/cluster pairs with many conditions
goLink | Get GO link
input.data | Input Data example
read.CPDBv2 | Read output from CellPhoneDB v2.
read.customInput | Read custom input file and re-structure it with InterCellar format
read.SCsignalR | Read output from SingleCellSignalR
run_app | Run the Shiny Application
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 unchanged the R-R and L-L