RunCellToCellSpatial.RdRunCellToCellSpatial
RunCellToCellSpatial( sys.small, ground.truth, assay, meta.data.to.map, edgelist, 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 NICHES objects |
| edgelist | data.frame. Each row is an directional edge between two spatially connected cells |
| 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 |