Fig. 3: Results of tree reconstruction methods on real C. elegans datasets.

Source data are provided as a Source Data file. a The ground truth lineage of C. elegans at L1 larvae stage. There are 363 profiled cells on the tree, while the original L1 larvae lineage has 668 cells. The tree pruning is performed using the ape package in R and the clonal relations between cells are preserved. The tree is visualized using iTOL⁴². b 2-D PCA visualization of the gene expression of the C. elegans data. After PCA, the first 20 PCs are used for K-means clustering and Slingshot to determine cell states and state trajectories (cell state tree). A detailed description of the processing steps for the gene expression data can be found in Supplementary Note 2. c Evaluating result on the C. elegans dataset with simulated barcodes. The methods are tested for varying mutation rates with dropout effects. Three metrics, RF distance (lower is better), Nye similarity (higher is better), and CID (lower is better) are presented. For all boxplots shown in the figure, we adopt the following default settings in the ggplot2 library: center line, median; Upper and lower box limits, the 25th and 75th percentiles; whiskers, 1.5× interquartile range for both upper and lower ends.