Figure 2.

(A) Major planarian cell types: epidermis, neurons (including a range of neuron subtypes), muscle (including body and pharynx muscle), parenchymal cell types (also known as cathepsin + cells, including a range of cell types), gut phagocytes, gut goblet cells, secretory cells (including a range of subtypes), protonephridia (including flame and tubule cells), and the pharynx cell type. (B) Schematics of lineage reconstruction by PArtition-based Graph Abstraction (PAGA). One way to represent single cell datasets is constructing a kNN graph that connects each cell to its k nearest neighbours in the single cell transcriptomic space. PAGA uses this graph to reconstruct the differentiation lineages. PAGA evaluates the connectivity between different clusters at the kNN graph level. Essentially, the connectivity arises by the existence of cells that are in an intermediate state between both cell clusters, suggesting that cells from one cluster can differentiate into other cell clusters. This reveals the likely connections between clusters and associates a P-value to each connection. (C) schematisation of the PAGA based planarian lineage reconstruction of the major planarian cell types, based on Plass et al. [19].