Add GESECA Scores to SpaMTP Object — addGesecaScores • SpaMTP

Adds Feature Set Enrichment Score for a specific pathway to a SpaMTP Seurat object's metadata. This is a helper function for PlotPathwaysSpatially.

Usage

addGesecaScores(
  pathways,
  object,
  assay = SeuratObject::DefaultAssay(object),
  slot = "scale.data",
  prefix = "",
  scale = FALSE
)

Arguments

pathways: List of gene/metabolite sets where the list names (pathway name) become metadata column names.
object: SpaMTP Seurat object to add the pathway scores to.
assay: Character string defining the name of assay to use for data extraction (default = `SeuratObject::DefaultAssay(object)).
slot: Character string stating the name of slot to extract data from (default = "scale.data").
prefix: Character string to append before each pathway name in metadata columns (default = "").
scale: Boolean logical value indicating whether to scale the GESECA score (default = FALSE).

Value

SpaMTP Seurat object with added GESECA scores in metadata.

Examples

### HELPER FUNCTION
#glycolysis_list <- list("Glycolysis" = c("RAMP_C_000218730","RAMP_G_000012583","RAMP_G_000001171","RAMP_G_000007564","RAMP_C_000218226","RAMP_C_000040403","RAMP_C_000001115","RAMP_G_000008859"))
#spamtp_obj <- addGesecaScores(pathways = glycolysis_list, object = spamtp_obj ,assay = "RNA", scale = TRUE)