Fig. 7.

scDesign2 guides the choice of sequencing depth in cell clustering. scDesign2 generates synthetic 10x Genomics data with fifteen sequencing depths. Two cell clustering methods—Seurat and SC3—are applied to each synthetic dataset to partition cells into cell clusters. a t-SNE visualization of four synthetic datasets, where cells are labeled by Seurat clusters (top), SC3 clusters (middle), and annotated cell types (bottom). b Two clustering accuracy measures (AMI and ARI) vs. sequencing depth; left: Seurat; right: SC3. In b, the results of the four sequencing depths in a are marked as dots and in the top, and the sequencing depth of the real dataset [83] is marked as vertical dashed lines