insitupy.plotting.overview

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insitupy.plotting.overview#

insitupy.plotting.overview(data, cells_layer=None, columns_to_plot=[], layer=None, force_layer=False, index=True, qc_width=3.0, fontsize=10, savepath=None, save_only=False, dpi_save=300)#

Plots an overview table with metadata and quality control metrics.

Parameters:

  • data (InSituExperiment) – The experiment object containing datasets and metadata.

  • cells_layer (Optional[str] (default: None)) – The layer of cells to use. Defaults to None.

  • columns_to_plot (List[str] (default: [])) – List of column names to include in the plot.

  • layer (str (default: None)) – The layer of the AnnData object to use for calculations. If None, the function will use the main matrix (adata.X) or the ‘counts’ layer if the main matrix does not contain integer counts.

  • force_layer (bool (default: False)) – Whether to use specified layer even if not integers in count matrix.

  • index (bool (default: True)) – Whether to add extra index or not. Default is True.

  • qc_width (float (default: 3.0)) – Width for quality control metric columns. Default is 3.0.

  • fontsize (int (default: 10)) – Font size for all text in the table. Default is 10.

  • savepath (Union[str, PathLike, Path] (default: None)) – Path to save the figure. Defaults to None.

  • save_only (bool (default: False)) – If True, only save without displaying. Defaults to False.

  • dpi_save (int (default: 300)) – DPI for saved figure. Defaults to 300.

Raises:

ImportError – If the ‘plottable’ framework is not installed.

Returns:

Displays a plot with the overview table.

Return type:

None

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