Fig 1.
Schematic of the Tempora algorithm.
Fig 2.
Tempora analysis of the HSMM data set.
a. Tempora trajectory built on clusters in the HSMM data set. b-c. Time-dependent pathways in the HSMM data set identified by Tempora’s pathway exploration feature. Blue dots represent clusters/cell types, the black line is the best fit of a generalized additive model (GAM) on the pathway enrichment scores of each pathway across all clusters, and grey areas depict 95% confidence intervals of the fitted model.
Fig 3.
Tempora analysis of the murine cortex data set.
a. Tempora trajectory built on clusters in the murine cerebral cortex data set. b-e. Time-dependent pathways in the murine cerebral cortex data set identified by Tempora’s pathway exploration feature. Blue dots represent clusters/cell types, the black line is the best fit of a generalized additive model (GAM) on the pathway enrichment scores of each pathway across all clusters, and grey areas depict 95% confidence intervals of the fitted model.
Fig 4.
Tempora analysis of the murine cerebellar data set.
a. Tempora trajectory built on clusters in the murine cerebellar data set. b-d. Time-dependent pathways in the murine cerebral cortex data set identified by Tempora’s pathway exploration feature. Blue dots represent clusters/cell types, the black line is the best fit of a generalized additive model (GAM) on the pathway enrichment scores of each pathway across all clusters, and grey areas depict 95% confidence intervals of the fitted model.
Fig 5.
Performance evaluation on the HSMM data set.
a-c. Trajectories of the HSMM data set inferred by by a. PAGA, b. Slingshot, c. TSCAN, d. Monocle 3 and e. CSHMM. f. The gold standard trajectory used to evaluate the accuracy of all inferred trajectories. g. Mismatch scores and h. accuracy scores of trajectories from the evaluated methods.
Fig 6.
Performance evaluation on the murine cerebral cortex data set.
a-c. Trajectories of the murine cerebral cortex data set inferred by by a. TSCAN, b. PAGA, c. Slingshot, d. Monocle 3 and e. CSHMM. f. The gold standard trajectory used to evaluate the accuracy of all inferred trajectories. g. Mismatch scores and h. accuracy scores of trajectories from the evaluated methods.
Fig 7.
Performance evaluation on the murine cerebellar data set.
a-e. Trajectories of the murine cerebellar data set inferred by a. TSCAN, b. PAGA, c. Slingshot, d. Monocle 3. e. The gold standard trajectory used to evaluate the accuracy of all inferred trajectories. f. Mismatch scores and g. accuracy scores of trajectories from the evaluated methods.
Fig 8.
Performance evaluation of Tempora with and without pathway enrichment analysis (PEA).
a-c. Trajectory inferred by Tempora without PEA of the a. HSMM, b. murine cerebral cortex and c. murine cerebellum data set. d. Accuracy scores and e. mismatch scores of Tempora trajectories with and without PEA.