add warning for no DA regions (46fa8f4f) · Commits · github_fork / DAseq2

R/getDAregion.R

+11 −7

Original line number	Diff line number	Diff line
		@@ -69,7 +69,7 @@ getDAregion <- function(
		assay.used = DefaultAssay(X.S), key = "PC_"
		)
		X.S <- FindNeighbors(X.S, reduction = "pca", dims = 1:n.dims, prune.SNN = prune.SNN, verbose = F)
		if(length(da.cells$da.up) > 0){
		if(length(da.cells$da.up) > 1){
		up.S <- CreateSeuratObject(
		counts = t(X[da.cells$da.up,])
		)
		@@ -90,7 +90,7 @@ getDAregion <- function(
		}
		n.up.clusters <- length(unique(up.clusters)) - as.numeric(0 %in% up.clusters)

		if(length(da.cells$da.down) > 0){
		if(length(da.cells$da.down) > 1){
		down.S <- CreateSeuratObject(
		counts = t(X[da.cells$da.down,])
		)
		@@ -131,12 +131,16 @@ getDAregion <- function(
		X.n.da <- length(unique(da.region.label)) - 1
		X.da.stat <- matrix(0, nrow = X.n.da, ncol = 3)
		colnames(X.da.stat) <- c("DA.score","pval.wilcoxon","pval.ttest")
		if(X.n.da > 0){
		for(ii in 1:X.n.da){
		X.da.stat[ii,] <- getDAscore(
		cell.labels = cell.labels, cell.idx = which(da.region.label == ii),
		labels.1 = labels.1, labels.2 = labels.2
		)
		}
		} else {
		warning("No DA regions found.")
		}

		if(do.plot & is.null(plot.embedding)){
		warning("plot.embedding must be provided by user if do.plot = T")