Fig. 2

Robustness of lineage and pseudotime inference methods: HSMM dataset. We examine the stability of three lineage and pseudotime inference approaches on the single-lineage HSMM dataset of [3], showing how each method orders the cells for the original dataset, as well as for 50 subsamples of the data. Panel (a): Monocle identifies the longest path through an MST constructed on all cells (red). Waterfall and TSCAN cluster cells and connect cluster centers with an MST (purple, clustering performed by k-means with k=5). Embeddr and Slingshot order cells using a principal curve, i.e., a non-linear fit through the data (green). As in [3], dimensionality reduction is performed by ICA. Panel (b): Scatterplots of pseudotimes based on 50 subsamples of the data vs. pseudotimes for the original dataset. Subsamples were generated in a bootstrap-like manner, by randomly sampling n times, with replacement from the original cell-level data and retaining only one instance of each cell. Thus, subsamples were of variable sizes, but contained on average about 63% of the original cells. The cluster-based MST method occasionally detected spurious branching events and, for the purpose of visualization, cells not placed along the main lineage were assigned a pseudotime value of 0