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Fig. 3 | Genome Biology

Fig. 3

From: PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Fig. 3

PAGA applied to a whole adult animal. a PAGA graphs for data for the flatworm Schmidtea mediterranea [13] at tissue, cell type, and single-cell resolution. We obtained a topologically meaningful embedding by initializing a single-cell embedding with the embedding of the cell-type PAGA graph. Note that the PAGA graph is the same as in Reference [13], only that here, we neither highlight a tree subgraph nor used the corresponding tree layout for visualization. b Established manifold learning for the same data violate the topological structure. c, d Predictions of RNA velocity evaluated with PAGA for two example lineages: epidermis and muscle. We show the RNA velocity arrows plotted on a single-cell embedding, the standard PAGA graph representing the topological information (only epidermis), and the PAGA graph representing the RNA velocity information

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