Plotting (sch.pl)
=================

The plotting module provides visualization functions for all analysis results.

Energy Plots
------------

.. currentmodule:: scHopfield.plotting

.. autosummary::
   :toctree: generated/

   plot_energy_landscape
   plot_energy_components
   plot_energy_boxplots
   plot_energy_scatters

Network Plots
-------------

.. autosummary::
   :toctree: generated/

   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

Jacobian Plots
--------------

.. autosummary::
   :toctree: generated/

   plot_jacobian_eigenvalue_spectrum
   plot_jacobian_eigenvalue_boxplots
   plot_jacobian_stats_boxplots
   plot_jacobian_element_grid

Correlation Plots
-----------------

.. autosummary::
   :toctree: generated/

   plot_gene_correlation_scatter
   plot_correlations_grid

Perturbation Plots
------------------

.. autosummary::
   :toctree: generated/

   plot_perturbation_effect_heatmap
   plot_perturbation_magnitude
   plot_gene_response
   plot_top_affected_genes_bar
   plot_simulation_comparison

Flow Plots
----------

.. autosummary::
   :toctree: generated/

   plot_reference_flow
   visualize_perturbation_flow

Other Plots
-----------

.. autosummary::
   :toctree: generated/

   plot_sigmoid_fit
   plot_trajectory