Fig. 2

PseudotimeDE captures the uncertainty in pseudotime inference. a Visualization of synthetic single-lineage cells marked with inferred pseudotime by Slingshot (using PCA). The black curve denotes the inferred lineage. b The distributions of individual cells’ inferred pseudotime by Slingshot across subsamples. In the vertical axis, cells are ordered by their true time in the lineage used in simulation; for every cell (a vertical coordinate), black dots have horizontal coordinates corresponding to the cell’s inferred pseudotime in the subsamples that include the cell. The more horizontally spread out the black dots, the greater uncertainty the pseudotime inference has. c Visualization of synthetic single-lineage cells marked with inferred pseudotime by Monocle3-PI (using UMAP). The black curve denotes the inferred lineage. Compared with (a), the inferred lineage is more wiggling. d The distributions of individual cells’ inferred pseudotime by Monocle3-PI across subsamples. Compared with (b), the uncertainty in pseudotime inference is greater. e Visualization of synthetic bifurcating cells marked with inferred pseudotime by Monocle3-PI (using UMAP). Monocle3-PI recovers the bifurcation topology. f Visualization of ten subsamples of the cells in (e), marked with inferred pseudotime by Monocle3-PI (using UMAP) on each subsample. Four out of the ten subsamples do not have the bifurcation topology correctly inferred (labeled with red “F”), revealing the uncertainty in pseudotime inference by Monocle3-PI. In panels a, c, e, and f, inferred pseudotime is represented by a color scale from 0 (the earliest pseudotime) to 1 (the latest pseudotime)