mdvtools.conversions
====================

.. py:module:: mdvtools.conversions


Functions
---------

.. autoapisummary::

   mdvtools.conversions.convert_scanpy_to_mdv
   mdvtools.conversions.convert_mudata_to_mdv
   mdvtools.conversions.convert_vcf_to_df
   mdvtools.conversions.compute_vcf_end
   mdvtools.conversions.convert_vcf_to_mdv
   mdvtools.conversions.create_regulamentary_project
   mdvtools.conversions._create_dt_heatmap
   mdvtools.conversions._add_dims


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

.. py:function:: convert_scanpy_to_mdv(folder: str, scanpy_object: scanpy.AnnData, max_dims: int = 3, delete_existing: bool = False, label: str = '') -> mdvtools.mdvproject.MDVProject

   Convert a Scanpy AnnData object to MDV (Multi-Dimensional Viewer) format.

   This function transforms single-cell RNA sequencing data from AnnData format into
   the MDV project structure, handling both cells and genes as separate datasources
   with their associated dimensionality reductions and metadata.

   :param folder: Path to the target MDV project folder
   :type folder: str
   :param scanpy_object: The AnnData object containing the single-cell data
   :type scanpy_object: AnnData
   :param max_dims: Maximum number of dimensions to include from
                    dimensionality reductions. Defaults to 3.
   :type max_dims: int, optional
   :param delete_existing: Whether to delete existing project data.
                           If False, merges with existing data. Defaults to False.
   :type delete_existing: bool, optional
   :param label: Prefix to add to datasource names and metadata columns
                 when merging with existing data. Defaults to "".
   :type label: str, optional

   :returns: The configured MDV project object with the converted data
   :rtype: MDVProject

   .. rubric:: Notes

   Data Structure Creation:
   - Creates two main datasources: '{label}cells' and '{label}genes'
   - Preserves all cell metadata from scanpy_object.obs
   - Preserves all gene metadata from scanpy_object.var
   - Transfers dimension reductions from obsm/varm matrices
   - Links cells and genes through expression data
   - Adds gene expression scores as a subgroup

   View Handling:
   - If delete_existing=True:
       * Creates new default view with empty initial charts
       * Sets project as editable
   - If delete_existing=False:
       * Preserves existing views
       * Updates views with new datasources
       * Maintains panel widths and other view settings
       * Adds new datasources to each view's initialCharts

   Dimension Reduction:
   - Processes dimensionality reductions up to max_dims
   - Supports standard formats (e.g., PCA, UMAP, t-SNE)
   - Column names in the format: {reduction_name}_{dimension_number}

   :raises ValueError: If the provided AnnData object is invalid or missing required components
   :raises IOError: If there are issues with file operations in the target folder
   :raises Exception: For other unexpected errors during conversion


.. py:function:: convert_mudata_to_mdv(folder: str, mudata_object: mudata.MuData, max_dims=3) -> mdvtools.mdvproject.MDVProject

.. py:function:: convert_vcf_to_df(vcf_filename: str) -> pandas.DataFrame

.. py:function:: compute_vcf_end(df: pandas.DataFrame) -> pandas.DataFrame

   Compute the end position of the variant determined from 'POS', 'REF' and 'ALT'.

   This is added as a column 'END' in the given DataFrame.


.. py:function:: convert_vcf_to_mdv(folder: str, vcf_filename: str) -> mdvtools.mdvproject.MDVProject

   Converts a VCF file to an MDV project.
   The VCF file must be tab-delimited, with the header lines starting with "##" and
   column names in the line starting with "#CHROM".

   An 'END' column is derived, which is the end position of the variant determined from 'POS', 'REF' and 'ALT'.


.. py:function:: create_regulamentary_project(folder, output: str, name: str, bigwig_folder='', bed_folder='', openchrome='DNase', openchrome_color='#eb9234', marks=['H3K4me1', 'H3K4me3', 'H3K27ac', 'CTCF'], mark_colors=['#349beb', '#3aeb34', '#c4c41f', '#ab321a'], genome='hg38')

.. py:function:: _create_dt_heatmap(folder, project, mdv, marks)

.. py:function:: _add_dims(table, dims, max_dims)