Fig. 2
From: Consequences and opportunities arising due to sparser single-cell RNA-seq datasets
A, B Cells plotted against the first two principle components of the AD dataset [20]. A PCA based on binary representation, and B PCA based on count representation. UMAP generated from data presented with C the binary-based PCs and D the count-based PCs. Colors indicate annotated cell type. E, H UMAP based on the count based PCs, in which cells are colored according to the binary representation of the marker genes AQP4 (E) and TNR (H) which are known markers for astrocytes and OPCs respectively [21]. F, G Similar as E and H but showing the normalized expression of the marker gene. I The performance (median F1-score) of cell type identification by SingleR [22] and scPred [23] when applied to binary (binarized data), normalized (normalized expression), and shuffled (shuffled normalized expression) for 22 datasets