schist.plotting
===============

.. py:module:: schist.plotting


Functions
---------

.. autoapisummary::

   schist.plotting.alluvial
   schist.plotting.draw_tree


Package Contents
----------------

.. py:function:: alluvial(adata: anndata.AnnData, level_start: int = 1, level_end: int = None, key: str = 'nsbm', gap: float = 0.05, legend_fontsize: Union[int, float, Literal['xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large']] = None, legend_fontweight: Union[int, Literal['light', 'normal', 'medium', 'semibold', 'bold', 'heavy', 'black']] = 'bold', axis_fontsize: Union[int, float, Literal['xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large']] = None, axis_fontweight: Union[int, Literal['light', 'normal', 'medium', 'semibold', 'bold', 'heavy', 'black']] = 'bold')

   Generate an alluvial plot for NSBM hierarchy

   This plot may be useful to study the hierarchical relations in a Nested
   Model generated by `scnbsm.inference.nested_model`.    Note that the `level_end`

   Parameters
   ----------
   adata
       The annotated data matrix.
   level_start
       The deepest level in the hierarchy (i.e. the one with more clusters)
       Note that this parameter marks the leafs of the tree
   level_end
       The coarser level in hierarchy. Default value is `None`, if pruning has not
       been performed, it may be useful to exclude uninformative levels anyway    
       Note that this parameter marks the root of the tree
   key
       The key used to group cells. Default is `nsbm`
   gap
       The gap between groups in percentage


.. py:function:: draw_tree(adata: anndata.AnnData, level: Union[str, int, None] = None, color: Union[str, None] = None, color_map: Union[matplotlib.colors.Colormap, str, None] = None, model_key: str = 'nsbm', ax: matplotlib.axes.Axes = None, show: bool = True, use_backend: str = None, save: Union[str, None] = None)

   Plots NSBM hierarchy using graph-tool capabilities

   Parameters
   ----------
   adata
       The annotated data matrix.
   level
       The NSBM level to be plot.    
   color
       The `adata.obs` property used to generate color. It is mutually exclusive
       with `level` option.
   color_map
       Th colormap to use for continuous colors
   save
       Name of the output file. If a non interactive notebook is detected, 
       this parameter is automatically set.    
   model_key
       The key used to perform nsbm