ovrlpy.run
==========

.. py:function:: ovrlpy.run(df, n_expected_celltypes=None, cell_diameter=10, min_expression = 1.0, signature_matrix=None, fit_umap = True, patch_length = 500, n_workers = min(8, len(os.sched_getaffinity(0))), umap_kwargs=UMAP_2D_PARAMS, cumap_kwargs=UMAP_RGB_PARAMS)

   This is a wrapper function that computes the integrity map for a given spatial
   transcriptomics dataset.
   It includes the entire ovrlpy pipeline, returning a integrity map and a signal
   strength map and produces a visualizer object that can be used to plot the results.

   :param df: The spatial transcriptomics dataset.
              This dataframe should contain a *gene*, *x*, *y*, and *z* column.
   :type df: pandas.DataFrame
   :param n_expected_celltypes: A rough estimate of expected cell type clusters.
                                A higher number will lead to a more disjoint UMAP embedding and a higher
                                detection of overlap events.
                                Defaults to None, which will use a heuristic on the PCA explained variance to determine cluster count.
   :type n_expected_celltypes: int, optional
   :param cell_diameter: The expected diameter of the cell/structure of interest in the sample.
                         Defaults to 10.
   :type cell_diameter: float, optional
   :param min_expression: A threshold value to discard areas with low expression, by default 5
                          Can be interpreted as: The minimum number of transcripts to appear within a
                          radius of 'KDE_bandwidth' for a region to be considered containing a cell.
   :type min_expression: int, optional
   :param signature_matrix: A celltypes x gene table of expression signatures to use to annotate the UMAP.
   :type signature_matrix: pandas.DataFrame, optional
   :param fit_umap: Whether to fit the UMAP to the data.
   :type fit_umap: bool
   :param patch_length: Size of the length in each dimension when calculating signal integrity in patches.
                        Smaller values will use less memory, but may take longer to compute.
   :type patch_length: int
   :param n_workers: The number of workers to use for processsing.
   :type n_workers: int
   :param umap_kwargs: Additional keyword arguments for the 2D UMAP embedding.
   :type umap_kwargs: dict, optional
   :param cumap_kwargs: Additional keyword arguments for the 3D UMAP embedding.
   :type cumap_kwargs: dict, optional

   :returns: * **integrity_map** (*numpy.ndarray*) -- A integrity pixel map of the spatial transcriptomics dataset.
             * **signal_map** (*numpy.ndarray*) -- A pixel map of the spatial transcriptomics dataset containing the detected signal.
             * **vis** (*Visualizer*) -- A visualizer object that can be used to plot the
               results of the integrity map