RunCellToCell.RdPerforms cell-cell transformation on a Seurat object, with structural downsampling to avoid data-inflation. Outputs another Seurat object, but where the columns of the matrix are barcode-barcode pairs, and the rows of the matrix are ligand-receptor mechanisms. This allows rapid manipulation and dimensional reduction of cell-cell connectivity data. The default assay of this object is called "CellToCell" to distinguish it from normal Seurat objects. Meta.data slots by default contain "SendingType" "ReceivingType" and "VectorType" information.
RunCellToCell(sys.small, ground.truth, assay, meta.data.to.map, output_format)
| sys.small | A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings. |
|---|---|
| ground.truth | Ground truth signaling mechanisms present in sys.small. |
| assay | The assay to run the SCC transformation on. Defaults to "RNA." |
| meta.data.to.map | A character vector of metadata names present in the original object which will be carried to the SCC objects |
| output_format | string. Choice of the output format. "seurat" will output a list of seurat objects, "raw" will output a list of lists with raw interaction matrix and compiled metadata |