Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
Fig 3
Rational initialization, minimal kmeans post-processing iterations, and merging give fast convergence.
We use the hand-gated CyTOF data for illustration. The data space is first partitioned into 50 hyperrectangles, which is about twice (recommended setting) the expected number of subpopulations (24). Next, the number of kmeans iterations was varied followed by flowMeans style merging. The convergence of PAC toward the hand-gated results, or ground truth, is fast due to the informative anchoring of cluster centers around high-density regions by the rational initialization. It takes less than 50 post-processing kmeans iterations for the PAC to achieve convergence. This efficiency allows the PAC method to scale to handle the clustering of large samples.