Getting Started
User Guide & Examples
sch
API Reference
fit_all_sigmoids()
compute_sigmoid()
fit_interactions()
compute_energies()
decompose_degradation_energy()
decompose_bias_energy()
decompose_interaction_energy()
network_correlations()
get_network_links()
compute_network_centrality()
get_top_genes_table()
compute_eigenanalysis()
get_top_eigenvector_genes()
get_eigenanalysis_table()
energy_gene_correlation()
celltype_correlation()
future_celltype_correlation()
get_correlation_table()
compute_umap()
energy_embedding()
save_embedding()
load_embedding()
compute_jacobians()
save_jacobians()
load_jacobians()
compute_jacobian_stats()
compute_jacobian_elements()
compute_rotational_part()
compute_reconstructed_velocity()
validate_velocity()
plot_energy_landscape()
plot_energy_components()
plot_energy_boxplots()
plot_energy_scatters()
plot_interaction_matrix()
plot_network_centrality_rank()
plot_centrality_comparison()
plot_gene_centrality()
plot_centrality_scatter()
plot_eigenvalue_spectrum()
plot_eigenvector_components()
plot_eigenanalysis_grid()
plot_grn_network()
plot_grn_subset()
plot_jacobian_eigenvalue_spectrum()
plot_jacobian_eigenvalue_boxplots()
plot_jacobian_stats_boxplots()
plot_jacobian_element_grid()
plot_gene_correlation_scatter()
plot_correlations_grid()
plot_perturbation_effect_heatmap()
plot_perturbation_magnitude()
plot_gene_response()
plot_top_affected_genes_bar()
plot_simulation_comparison()
plot_reference_flow()
visualize_perturbation_flow()
plot_sigmoid_fit()
plot_trajectory()
ODESolver
create_solver()
simulate_trajectory()
simulate_perturbation()
simulate_shift()
calculate_perturbation_effect_scores()
calculate_cell_transition_scores()
get_top_affected_genes()
compare_perturbations()
Additional Information
Plot all energy components (total, interaction, degradation, bias) for a cluster.
adata (AnnData) – Annotated data object
cluster (str) – Cluster name
basis (str, optional) – Embedding basis
Figure with subplots
plt.Figure