Extended Data Fig. 6: Comparing pseudotime inferred from neighborhood V(D)J space or GEX space.

a, Pearson’s correlation coefficients of pseudotime order and average relative TRAV location over sliding windows of 30 adjacent neighborhoods on the pseudotime order (left: pseudotime inferred from neighborhood V(D)J space; right: pseudotime inferred from neighborhood GEX space). Y-axis is the correlation coefficient and the x-axis is the median pseudotime order of the 30 adjacent neighborhoods. The color of the points represents statistical significance (orange: P-value from the Pearson’s correlation < 0.05; blue: P-value ≥ 0.05). The red dashed lines mark the correlation coefficient of 0. b, The same plot as in a but for TRAJ. c, Scatterplots of branch probability to CD8+ T against pseudotime in abT(entry) cells. Each point represents a cell. Top panel: pseudotime inferred from neighborhood V(D)J space as in Fig. 4a top panel. Bottom panel: pseudotime inferred from neighborhood GEX space as in Fig. 4a bottom right panel. d, Volcano plot summarizing results of TFs that are correlated with branch probabilities to CD8+ T lineage in V(D)J pseudotime within abT(entry) cells. The y-axis is the -log₁₀(BH adjusted P-value) and the x-axis is the correlation coefficient. Labeled TFs that had significant (BH adjusted P-value < 0.05) positive correlations (correlation coefficient > 0.1) were colored in red, the ones with significant negative correlations (correlation coefficient < −0.1) were colored in blue, and the rest were colored in black.