atlas_protocol_scripts.pl.plot_paired#

atlas_protocol_scripts.pl.plot_paired(adata, groupby, *, paired_by=None, var_names=None, show=True, return_fig=False, n_cols=4, panel_size=(3, 4), show_legend=False, hue=None, size=10, ylabel='expression', pvalues=None, pvalue_template=<function <lambda>>, adjust_fdr=False, boxplot_properties=None)#

Pairwise expression plot.Makes on panel with a paired scatterplot for each variable.

Parameters

  • adata – adata matrix (usually pseudobulk).

  • groupby – Column containing the grouping. Must contain exactely two different values.

  • paired_by (default: None) – Column indicating the pairing (e.g. “patient”)

  • var_names (default: None) – Only plot these variables. Default is to plot all.

  • adjust_fdr (default: False) – Adjust p-values for multiple testing using the Benjamini-Hochberg procedure.

  • boxplot_properties (default: None) – Properties to pass to the boxplot function.

  • hue (default: None) – Column indicating the hue.

  • n_cols (default: 4) – Number of columns in the figure.

  • panel_size (default: (3, 4)) – Size of each panel.

  • pvalue_template (default: <function <lambda> at 0x7f45b76bb370>) – Template for the p-value annotation. Must contain a single placeholder for the p-value.

  • pvalues (Optional[Sequence[float]] (default: None)) – P-values to annotate. Must be the same length as var_names.

  • return_fig (default: False) – Return the figure object.

  • show (default: True) – Show the figure.

  • show_legend (default: False) – Show the legend.

  • size (default: 10) – Size of the points.

  • ylabel (default: 'expression') – Label for the y-axis.