A diffusion process is used to smooth genes<U+2019> expression values based on their neighbors<U+2019> defined in a high-confidence experimentally validated protein-protein network.
projectData(
object,
adjMatrix,
alpha = 0.5,
normalizeAdjMatrix = c("rows", "columns")
)CellChat object
adjacency matrix of protein-protein interaction network to use
numeric in [0,1] alpha = 0: no smoothing; a larger value alpha results in increasing levels of smoothing.
how to normalize the adjacency matrix possible values are 'rows' (in-degree) and 'columns' (out-degree)
a projected gene expression matrix
This function is useful when analyzing single-cell data with shallow sequencing depth because the projection reduces the dropout effects of signaling genes, in particular for possible zero expression of subunits of ligands/receptors