merquaco.figures.plot_full_pixel_fig

merquaco.figures.plot_full_pixel_fig(pixel_classification: ndarray, dapi_mask_input: ndarray | str | Path, transcripts_mask_input: ndarray | str | Path, detachment_mask_input: ndarray | str | Path, transcripts_percent: int | float, detachment_percent: int | float, damage_mask_input: ndarray | str | Path = None, ventricle_mask_input: ndarray | str | Path = None, damage_percent: float = nan, ventricle_percent: float = nan, out_file: str | Path = '', dpi: int = 200)

Plots full pixel classification figure with pixel classification, pixel percentages, and all binary masks.

Parameters:

  • pixel_classification (np.ndarray) – Array of pixel classification results

  • transcripts_mask_input (np.ndarray, str, or Path) – Array of or path to transcripts mask

  • detachment_mask_input (np.ndarray, str, or Path) – Array of or path to detachment mask

  • transcripts_percent (int or float) – Percent of ideal tissue area classified as transcripts

  • detachment_percent (int or float) – Percent of ideal tissue area classified as detachment

  • damage_mask_input (np.ndarray, str, or Path, optional) – Array of or path to damage mask. Default is None.

  • ventricle_mask_input (np.ndarray, str, or Path, optional) – Array of or path to ventricle mask. Default is None.

  • damage_percent (int or float, optoinal) – Percent of ideal tissue area classified as damage. Default is np.nan.

  • ventricle_percent (int or float, optoinal) – Percent of ideal tissue area classified as ventricles. Default is np.nan.

  • out_file (str or Path, optional) – Path at which to save plot. Default is ‘’.

  • dpi (int, optional) – DPI value for plotting. Default is 200.

Return type:

None

Raises:

ValueError – If only one of [‘damage_mask’, ‘ventricle_mask’] is passed.