Fig. 4

Comparison of accuracy scores for lineage and pseudotime inference methods: Simulated datasets. Gaussian kernel density plots of accuracy scores show how five lineage inference methods performed on a series of simulated datasets with two different topologies: Panels (a,c) two lineages and Panels (b,d) five lineages. In both settings, the simulated data contained variable numbers of cells and levels of noise. Bars to the left of each density plot represent the percentage of datasets on which a method returned an error. Errors are treated as 0 values for calculating the median score, but are not included in the density estimates. Monocle, Monocle 2, DPT, and TSCAN were implemented in several ways and these densities represent the best results obtained by each method. Slingshot was implemented with various dimensionality reduction techniques, chosen to match the best-case settings of the other methods and with clusters assigned by Gaussian mixture modeling (GMM). See Simulation study for the definition of accuracy scores based on Kendall’s rank correlation coefficient and Additional file 1 for details on simulation scenarios