troutpy.pl.logfoldratio_over_noise

troutpy.pl.logfoldratio_over_noise#

troutpy.pl.logfoldratio_over_noise(sdata, control_key='control_probe', test_method='auto', figures_path='', save=False, custom_plot_filename=None, palette='troutpy')#

Creates a violin plot comparing logfoldratio_over_noise values for controlvs non-control probes, and tests for significance using the specified test.

Parameters:

  • sdata (spatialdata.SpatialData) – SpatialData object that contains ‘xrna_metadata’ with ‘var’ DataFrame.

  • control_key (str) – The column in var indicating which probes are controls.

  • test_method (str) –

    Statistical test to use. Options:

    • ”t-test” → Welch’s t-test

    • ”mannwhitney” → Mann-Whitney U-test

    • ”auto” (default) → Chooses test based on normality test.

  • figures_path (str) – Directory to save the figure.

  • save (str) – If True, saves the figure as a PDF in the specified path.

  • custom_plot_filename (str) – Custom filename for the saved plot.

  • palette (str) – Matplotlib palette name or list of two colors. Default is [“lightgrey”, “black”].

Return type:

None

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