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[LindsayHayes]

I made a post for this in pretty plots section!

5. Gene_A x Gene_B Plot

If you want to check if the same cells express 2 different genes you can plot one gene on the x-axis and the other gene on the y-axis using the plot() function. From this code just update the gene names (here “Kdm5d” & “Uty”) to your 2 genes of interest! gene_A <- which(rowData(sce)[,2] %in% "Kdm5d") gene_B <- which(rowData(sce)[,2] %in% "Uty") plot(logcounts(sce)[gene_A,], logcounts(sce)[gene_B,], xlab="Kdm5d", ylab="Uty") The genes along the x-axis only express the gene_A, genes along the …