Fig. 3: Data integration, partition-based graph abstraction (PAGA) and diffusion pseudotime in scATAC-seq. | Nature Communications

Fig. 3: Data integration, partition-based graph abstraction (PAGA) and diffusion pseudotime in scATAC-seq.

From: EpiScanpy: integrated single-cell epigenomic analysis

Fig. 3

a UMAP with annotated cell types from scATAC-seq for blood cells from Satpathy et al.5, performed on the peak feature space (57,177 cells x 83,823 peaks). Only the broad cell type annotation is shown. b Joint UMAP for two scATAC-seq datasets with experiment label (10x Genomics and Satpathy et al.) for concatenated count matrices (left) and mixed using BBKNN with experiment label (middle) and cell type label (right) (62,284 cells x 123,280 peaks). c Force-directed graph drawing of the Satpathy et al. dataset. d PAGA plot for the same cells using the same Force-directed graph embedding. e Monocyte differentiation path depicted on top of the force-directed graph drawing, and f openness of peaks at marker genes during pseudotime progression (distance) in the monocyte differentiation path (16,004 cells x 83,823 peaks).

Back to article page