harreman.plots.plot_interacting_cell_scores

harreman.plots.plot_interacting_cell_scores#

harreman.plots.plot_interacting_cell_scores(adata, interactions=None, coords_obsm_key=None, test=None, only_sig_values=False, use_FDR=True, normalize_values=False, sample_specific=False, s=None, vmin=None, vmax=None, figsize=(10, 10), cmap='Reds', colorbar=True, swap_y_axis=False)[source]#

Plot spatial maps of interacting cell scores for selected gene pairs or metabolites.

Parameters:

  • adata (AnnData) – Must contain interacting cell statistics in: uns['interacting_cell_results'][test]['gp'/'m'].

  • interactions (list of str) – Gene pairs or metabolites to plot.

  • coords_obsm_key (str) – Key in adata.obsm containing spatial coordinates.

  • test ({"parametric", "non-parametric"}) – Determines which statistical results to load.

  • only_sig_values (bool, default False) – If True, plot only significant values (FDR or p-value).

  • use_FDR (bool, default True) – If only_sig_values=True, choose FDR instead of raw p-values.

  • normalize_values (bool, default False) – Apply per-interaction min–max normalization.

  • sample_specific (bool, default False) – Plot each sample separately, using uns['sample_key'].

  • s (float) – Dot size.

  • vmin (float or str ("p5", "p95"), optional) – Color scale limits; percentiles allowed.

  • vmax (float or str ("p5", "p95"), optional) – Color scale limits; percentiles allowed.

  • figsize (tuple, default (10,10)) – Figure size.

  • cmap (str, default "Reds") – Colormap for the score intensity.

  • colorbar (bool, default True) – Show or hide the colorbar.

  • swap_y_axis (bool, default False) – Flip the y-axis for visualization conventions.