Update UMI_gene_perCell_plot_v3.R (4c19d351) · Commits · github_fork / SHARE Seq AlignmentV2

UMI_gene_perCell_plot_v3.R

+2 −2

Original line number	Diff line number	Diff line
		@@ -45,7 +45,7 @@ if (length(unique(linear$V1)) < 20000){
		for (i in 1:nrow(window)){
		print(window[i, ])
		sub <- linear %>% filter(V1 %in% cells[window[i,1]:window[i,2]])
		Mx.sub <- as(acast(sub, V2~V1, value.var="V3", fill=0, fun.aggregate = mean), "sparseMatrix")
		Mx.sub <- as(acast(sub, V2~V1, value.var="V3", fill=0, fun.aggregate = sum), "sparseMatrix")
		emptygenes <- genes[!genes %in% rownames(Mx.sub)]
		emptyMx <- as(matrix(data = 0, ncol = ncol(Mx.sub), nrow = length(emptygenes)), "sparseMatrix")
		colnames(emptyMx) <- colnames(Mx.sub)
		@@ -58,7 +58,7 @@ if (length(unique(linear$V1)) < 20000){
		}
		}
		} else {
		Df2 <- as(acast(linear, V2~V1, value.var="V3", fill=0, fun.aggregate = mean), "sparseMatrix")
		Df2 <- as(acast(linear, V2~V1, value.var="V3", fill=0, fun.aggregate = sum), "sparseMatrix")
		}
		}
		print(paste("No. genes x cells = ", nrow(Df2), "x", ncol(Df2), sep=""))