Probabilities not adjusted when computing centrality on "netP"

[ycl6]

Based on the current netAnalysis_computeCentrality function, the prob values are adjusted if pval did not meet the thresh, i.e. set to 0 in L206.

CellChat/R/analysis.R

Lines 201 to 208 in 418b660

	netAnalysis_computeCentrality <- function(object = NULL, slot.name = "netP", net = NULL, net.name = NULL, thresh = 0.05) {
	if (is.null(net)) {
	prob <- methods::slot(object, slot.name)$prob
	pval <- methods::slot(object, slot.name)$pval
	pval[prob == 0] <- 1
	prob[pval >= thresh] <- 0
	net = prob
	}

However, pval is only provided and stored in net when running the computeCommunProb function.
The computeCommunProbPathway function only provides prob and not pval. Therefore methods::slot(object, "netP")$pval is NULL. The probabilities is not adjusted when slot.name = "netP".