Calculate communication scores between all cell type pairs mediated by metabolites. Communication strength represents the potential for signal transmission from sender to receiver cells via metabolites.
computeCommunication(
object,
method = "geometric",
min_production = 0.1,
min_sensing = 0.1,
population.size = FALSE,
n_permutations = 100,
n_cores = 1,
seed = 42,
verbose = TRUE
)A scMetaLink object with production and sensing scores
Character. Communication score method: "geometric" (default), "product", "harmonic"
Numeric. Minimum production score threshold (0-1)
Numeric. Minimum sensing score threshold (0-1)
Logical. Whether to weight communication by cell type population sizes. When TRUE, communication strength is scaled by the relative abundance of sender and receiver cell types, reflecting the biological reality that larger populations contribute more to overall tissue signaling.
Integer. Number of permutations for significance testing (0 to skip)
Integer. Number of cores for parallel computing
Integer. Random seed for reproducibility
Logical. Print progress messages
Updated scMetaLink object with communication_scores and p-values
The communication score combines production and sensing capabilities:
geometric: sqrt(production * sensing) - balanced measure
product: production * sensing - emphasizes strong bilateral signals
harmonic: 2*production*sensing/(production+sensing) - penalizes imbalance
When population.size = TRUE, scores are multiplied by:
sqrt(n_sender/n_total * n_receiver/n_total), which accounts for the
relative contribution of each cell type to tissue-level communication.