prism.annotate module

prism.annotate.run(input_fp, output_fp, bed_fps, annotation_names, output_figure_fp=None, dpi=400, width=4, height=4, scale=1, font_family=None)

prism.annotate.scatter_1d(subclone_assignments, num_subclones, depths, fingerprint_fractions, annotation_names, annotation_mask, width, height, dpi)

Generate annotated scatterplot for one-dimensional PRISM analysis.

Parameters:

• subclone_assignments (list) – List containing subclone assignment status for each fingerprint epilocus.
• num_subclones (int) – Number of subclones.
• depths (list) – List of depths (pattern counts).
• fingerprint_fractions (list) – List of fingerprint fractions.
• annotation_names (list) – List of the names of annotations.
• annotation_mask (list) – List containing annotation status for each fingerprint epilocus.
• width (float) – Figure width.
• height (float) – Figure height.
• dpi (int) – Figure DPI.

prism.annotate.scatter_2d(subclone_assignments, num_subclones, fingerprint_fractions, annotation_names, annotation_mask, width, height, dpi)

Generate annotated scatterplot for two-dimensional PRISM analysis.

Parameters:

• subclone_assignments (list) – List containing subclone assignment status for each fingerprint epilocus.
• num_subclones (int) – Number of subclones.
• fingerprint_fractions (list) – List of fingerprint fractions.
• annotation_names (list) – List of the names of annotations.
• annotation_mask (list) – List containing annotation status for each fingerprint epilocus.
• width (float) – Figure width.
• height (float) – Figure height.
• dpi (int) – Figure DPI.