Extended Data Fig. 4: Adjusting diffusion pseudotime map parameters for visualization of pseudotemporal trajectories.
From: Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq
a, Using a large number of diffusion pseudotime components yields a developmental trajectory that enhances separation of trajectories of different cell populations (n = 274,182 bone marrow cells). FLEs of single cell (colored by cell type annotation) generated from diffusion pseudotime maps (t = ∞) with 15 (left), 50 (middle) or 100 (right) components. CD8+ and CD4+ naïve T cells are fused together in the left FLE (circled in red). Erythrocytes and Pro-B cells are overlapped in the middle FLE (circled in Red). b, Choosing the timescale t for a diffusion pseudotime map. Von Neumann entropy (y axis) for diffusion maps with 100 components calculated from the bone marrow data at different timescales (x axis). Black point: knee point.
