Plotting (sch.pl)

The plotting module provides visualization functions for all analysis results.

Energy Plots

`plot_energy_landscape`(adata, cluster[, ...])	Plot energy landscape on embedding space.
`plot_energy_components`(adata, cluster[, basis])	Plot all energy components (total, interaction, degradation, bias) for a cluster.
`plot_energy_boxplots`(adata[, cluster_key, ...])	Plot energy distributions for different clusters using boxplots.
`plot_energy_scatters`(adata[, cluster_key, ...])	Plot energy landscapes for different clusters using 3D scatter plots.

`plot_interaction_matrix`(adata, cluster[, ...])	Plot interaction matrix heatmap.
`plot_network_centrality_rank`(adata[, ...])	Plot top genes ranked by network centrality score.
`plot_centrality_comparison`(adata, cluster1, ...)	Compare network centrality scores between two clusters.
`plot_gene_centrality`(adata, gene[, ...])	Plot network centrality scores for a specific gene across clusters.
`plot_centrality_scatter`(adata, x_metric, ...)	Plot scatter of two centrality metrics for all clusters.
`plot_eigenvalue_spectrum`(adata[, clusters, ...])	Plot eigenvalue spectrum in the complex plane.
`plot_eigenvector_components`(adata, cluster)	Plot sorted eigenvector components with top gene annotations.
`plot_eigenanalysis_grid`(adata[, ...])	Plot comprehensive eigenanalysis grid for all clusters.
`plot_grn_network`(adata, cluster[, genes, ...])	Generate a Gene Regulatory Network (GRN) graph for a cluster.
`plot_grn_subset`(adata, cluster, selected_genes)	Plot a Gene Regulatory Network (GRN) for a user-defined subset of genes.

`plot_jacobian_eigenvalue_spectrum`(adata[, ...])	Plot Jacobian eigenvalues in complex plane for each cluster.
`plot_jacobian_eigenvalue_boxplots`(adata[, ...])	Plot boxplots of positive real and imaginary parts of Jacobian eigenvalues.
`plot_jacobian_stats_boxplots`(adata[, ...])	Plot boxplots of Jacobian summary statistics.
`plot_jacobian_element_grid`(adata, gene_pairs)	Plot grid of Jacobian elements (partial derivatives) on UMAP.

`plot_gene_correlation_scatter`(adata, clus1, ...)	Plot scatter of gene correlations between two clusters.
`plot_correlations_grid`(adata[, cluster_key, ...])	Plot grid of correlation scatter plots between all pairs of clusters.

`plot_perturbation_effect_heatmap`(adata[, ...])	Plot heatmap of perturbation effects across clusters and genes.
`plot_perturbation_magnitude`(adata[, ...])	Plot perturbation magnitude on embedding and as boxplot.
`plot_gene_response`(adata, genes[, ...])	Plot expression change for specific genes across clusters.
`plot_top_affected_genes_bar`(adata[, ...])	Bar plot of top affected genes showing direction and magnitude.
`plot_simulation_comparison`(adata, gene[, ...])	Compare original and simulated expression for a gene.

`plot_reference_flow`(adata[, basis, ...])	Plot reference velocity flow (e.g., from scVelo).
`visualize_perturbation_flow`(adata[, basis, ...])	Create comprehensive visualization of perturbation flow analysis.

`plot_sigmoid_fit`(adata, gene[, spliced_key, ...])	Plot sigmoid fit for a gene showing expression CDF and fitted curve.
`plot_trajectory`(trajectory, t_span[, ...])	Plot gene expression trajectories over time.