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')#

Plot a violin plot comparing logfoldratio_over_noise for control vs non-control probes.

A statistical test is used to compare the two groups, and the result is annotated on the plot.

Parameters:

  • sdata (SpatialData) – SpatialData object that contains an xrna_metadata table with a var DataFrame.

  • control_key (str (default: 'control_probe')) – Column in sdata["xrna_metadata"].var indicating which probes are controls.

  • test_method (str (default: 'auto')) – Statistical test to use: "t-test" (Welch’s t-test), "mannwhitney" (Mann-Whitney U test), or "auto" to choose based on a Shapiro-Wilk normality test of both groups.

  • figures_path (str (default: '')) – Directory path to save the figure.

  • save (bool (default: False)) – Whether to save the figure.

  • custom_plot_filename (Optional[str] (default: None)) – Custom filename for saving the plot.

  • palette (str (default: 'troutpy')) – Two-color palette name, resolved via troutpy.pl.get_palette(). Falls back to a Matplotlib colormap, then to grey/black, if neither is found.

Return type:

None

Returns:

None

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