Calculate mean ligand expression as a data frame for plotting in circos plot — mean_ligand_expression • dominoSignal

Creates a data frame of mean ligand expression for use in plotting a circos plot of ligand expression and saving tables of mean expression. us

Usage

mean_ligand_expression(x, ligands, cell_ident, cell_barcodes, destination)

Arguments

x: Gene by cell expression matrix
ligands: Character vector of ligand genes to be quantified
cell_ident: Vector of cell type (identity) names for which to calculate mean ligand gene expression
cell_barcodes: Vector of cell barcodes (colnames of x) belonging to cell_ident to calculate mean expression across
destination: Name of the receptor with which each ligand interacts

Value

A data frame of ligand expression targeting the specified receptor

Examples

example(build_domino, echo = FALSE)
counts <- dom_counts(pbmc_dom_built_tiny)
mean_exp <- mean_ligand_expression(counts,
 ligands = c("PTPRC", "FASLG"), cell_ident = "CD14_monocyte",
 cell_barcodes = colnames(counts), destination = "FAS")