Saving for QC and results plots.

Some functions (e.g., cell2location.utils.filtering.filter_genes or RegressionModel.plot_QC) generate plots, but have no way (that I could think of) for saving the plots from a script. Workarounds don’t always work, for example the code below only saves one of the two plots generated when interactively running the code.

fig, ax = plt.subplots()
mod.plot_QC()
# only saves first plot unfortunately
fig.savefig(QC_dir / 'QC_plots_signature_model.png', dpi=300)

Since sometimes running cell2loc interactively is not practical, it would be great to have improved plot saving capabilities! Thank you for your great work!

[yozhikoff]

@yozhikoff what do you think is the best interface for saving plots? File path argument to the function or just making sure that mod.plot_QC() creates only one plot?

@vitkl I would just return a list of Figure objects, so that the user could do whatever is needed - save, modify, add something else.

[vitkl]

Also adding the history plots for completeness:

# plot ELBO loss history during training, removing first 100 epochs from the plot
mod.plot_history(5000)
plt.savefig(f"{scvi_run_name}/training_ELBO_history_minus5k.png",
                   bbox_inches='tight')
plt.close()
mod.plot_history(0)
plt.savefig(f"{scvi_run_name}/training_ELBO_history_all.png",
                   bbox_inches='tight')
plt.close()