RunCellToSystem.RdCondenses all signaling edges coming from each cell within a Seurat object connecting to every other cell in the system, treated as a single sink. Outputs another Seurat object, but where the rows of the matrix are ligand-receptor mechanisms and the columns are each a single sending cell barcode. The information in the matrix is an average (or a sum, depending on user preference) of all signaling edges coming from that particular cell, to every other cell in the system (including to itself.) This transformation allows rapid manipulation and dimensional reduction of how a cell is connected within the system. The default assay of this object is called "CellToSystem" to distinguish it from other Seurat objects. Meta.data slots by default contain "SendingType" information, which is the celltypes for each point, and "SendingCell" which is the exact cell barcode present in the original Seurat object.
RunCellToSystem( sys.small, ground.truth, assay, blend = "mean", 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 CellToSystem transformation on. Defaults to "RNA." |
| blend | Choice of linear operator to combine edges. Defaults to "mean", also accepts "sum" |
| meta.data.to.map | A character vector of metadata names present in the original object which will be carried to the NICHES 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 |