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Saving for QC and results plots.

See original GitHub issue

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()
# 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!

Issue Analytics

  • State:open
  • Created a year ago
  • Comments:7 (6 by maintainers)

github_iconTop GitHub Comments

yozhikoffcommented, Aug 16, 2022

@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.

vitklcommented, Aug 16, 2022

Also adding the history plots for completeness:

# plot ELBO loss history during training, removing first 100 epochs from the plot
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