Fig. 2

Ganglioglioma neoplastic cellular hierarchy. A Violin plots of neoplastic cell expression (log1p[RNA], base 2) of individual neuroectodermal markers by cluster (left) or by CD34 status (right). B Feature plot of ganglioglioma neoplastic tumor 1, 4, and 5 nuclei CellRank/CytoTRACE pseudotime (tumor 3 nuclei excluded due to low complexity which resulted in aberrantly high calculated pseudotime for tumor 3 nuclei). C, D Violin plots of CytoTRACE pseudotime by ganglioglioma cluster (C) or CD34 status (D). E Random walk of earliest pseudotime cells (black dots) via CellRank/CytoTRACE pseudotime to predicted terminal states (yellow dots). F–H Differentiation potency was also inferred via SCENT signaling entropy rate (SR) for ganglioglioma neoplastic nuclei. Feature and violin plots of SR shown analogous to B-D above for CytoTRACE pseudotime. I Signaling entropy rate versus CytoTRACE pseudotime for ganglioglioma neoplastic nuclei (except tumor 3), colored by CD34 status (CD34+ in blue, CD34− gray). Gray line represents linear least-squares fit to (all of the neoplastic) data, with gray shading representing the 95% confidence interval. J–L Neoplastic cell scVelo RNA velocity-derived pseudotimes by dynamical (J), stochastic (K), and steady state (L) modes. M RNA velocity steady state pseudotime vs CytoTRACE pseudotime, colored by CD34 status (CD34+ in blue, CD34− gray). Gray line represents linear least-squares fit to (all of the neoplastic) data, with gray shading representing the 95% confidence interval