Visualization of PAC vs. PAC-MAN results for blood, bone marrow, colon, inguinal lymph node, and liver samples.

The PAC (explorative clustering) and PAC-MAN (data-level cellular states) results are presented for each sample in column-wise fashion. Each tissue sample’s t-SNE plots were generated using 100,000 randomly drawn cell events for that sample. The results from PAC (top panel) and PAC-MAN (bottom panel) steps are presented in pairs. Initial PAC discovery was set to 50 subpopulations without advanced knowledge of the number of subpopulations in each sample. In MAN, 130 network clades (optimal number from elbow point analysis) were outputted, and the cellular states are defined by expression (marker signal), network structure, and dataset-level variation. This composite definition of cellular state naturally aggregates the PAC clusters to yield smaller number of subpopulations in less variable samples. S11 Fig is a higher resolution version of Fig 12 with subpopulation and clade labels.