troutpy.pp.format_adata

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troutpy.pp.format_adata#

troutpy.pp.format_adata(input_path, outpath_dummy, xlimits, ylimits)#

Processes and formats AnnData and transcripts by loading data, merging cell information,applying spatial filters, and saving the processed data to a dummy output directory.

Parameters:

  • input_path (str) – Path to the input directory containing:’cell_feature_matrix.h5’,’cells.parquet’,’transcripts.parquet’

  • outpath_dummy (str) – Path to the output directory where processed files will be saved.

  • xlimits (list) – Spatial limits for the x-coordinate filtering [min_x, max_x].

  • ylimits (list) – Spatial limits for the y-coordinate filtering [min_y, max_y].

Raises:

  • FileNotFoundError – If required input files are not found in the input_path.

  • ValueError – If xlimits or ylimits are not properly defined.

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