Fig. 1
From: Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Overview of the benchmark protocol. We ran five representative DR methods, systematically varying their parameters on a large grid of values, on ten scRNA-seq datasets with known cell identity. We evaluate their ability to map cells of a given identity near other cells of the same identity, as measured by the silhouette score and the AMI after k-means clustering in the representation space