CardamomOT.tools.plot_networks
==============================

.. py:module:: CardamomOT.tools.plot_networks

.. autoapi-nested-parse::

   Network analysis and visualisation utilities for inferred GRNs.



Functions
---------

.. autoapisummary::

   CardamomOT.tools.plot_networks.analyse_reseau
   CardamomOT.tools.plot_networks.reseau_top_regulateurs
   CardamomOT.tools.plot_networks.plot_network


Module Contents
---------------

.. py:function:: analyse_reseau(matrix, gene_names=None, top_regulateurs=10, top_cibles=10, width_scale=5)

   Plot per-regulator subgraphs for the top regulators in the GRN.

   :param matrix: G×G interaction matrix (positive = activation, negative = inhibition).
   :type matrix: np.ndarray or pd.DataFrame
   :param gene_names: Gene names matching matrix rows/columns.
   :type gene_names: list of str, optional
   :param top_regulateurs: Number of top regulators to show.
   :type top_regulateurs: int
   :param top_cibles: Number of top targets per regulator.
   :type top_cibles: int
   :param width_scale: Multiplier for edge width (proportional to |weight|).
   :type width_scale: float


.. py:function:: reseau_top_regulateurs(matrix, gene_names=None, name='Réseau réduit top régulateurs', top_regulators=10, top_targets_per_reg=8, leaf_threshold=0.0, width_scale=5)

   Draw a reduced GRN showing only top regulators and their top targets.

   :param matrix: G×G interaction matrix.
   :type matrix: np.ndarray or pd.DataFrame
   :param gene_names: Gene names matching matrix rows/columns.
   :type gene_names: list of str, optional
   :param name: Figure title.
   :type name: str
   :param top_regulators: Number of top regulators (by total outgoing strength).
   :type top_regulators: int
   :param top_targets_per_reg: Maximum targets per regulator.
   :type top_targets_per_reg: int
   :param leaf_threshold: Minimum absolute weight (as fraction of max) to include a target.
   :type leaf_threshold: float
   :param width_scale: Multiplier for edge width.
   :type width_scale: float

   :returns: The reduced graph.
   :rtype: nx.DiGraph


.. py:function:: plot_network(p, seuil=0.3, net_toplot='inter_simul', net_index=0, train='full', ns=1)

   Visualise the inferred GRN for a project directory.

   Loads ``net_toplot.npy`` and plots the top regulators using
   :func:`analyse_reseau` and :func:`reseau_top_regulateurs`.

   :param p: Path to the project directory (trailing slash included).
   :type p: str
   :param seuil: Edge-weight threshold passed as ``leaf_threshold`` to
                 :func:`reseau_top_regulateurs` (fraction of max weight).
   :type seuil: float
   :param net_index: Index along the third axis of ``net_toplot.npy`` to visualise
                     (default 0).
   :type net_index: int
   :param train: Data split used to recover gene names (``"full"`` or ``"train"``).
   :type train: str
   :param ns: Number of leading rows/columns to skip in ``net_toplot.npy``
              (default 1, which drops the basal/stimulus node).
   :type ns: int