Settings

A convenience function for setting some default matplotlib.rcParams and a high-resolution jupyter display backend useful for use in notebooks.

set_figure_params

Set resolution/size, styling and format of figures.

An object that allows configuring Scanpy.

settings

Settings for scanpy.

Some selected settings are discussed in the following.

Verbosity controls the amount of logging output:

Verbosity

Logging verbosity levels for scanpy.settings.verbosity.

Influence the global behavior of plotting functions. In non-interactive scripts, you’d usually want to set settings.autoshow to False.

settings.autoshow	Automatically show figures if autosave == False (default True).
settings.autosave	Automatically save figures in figdir (default False).

The default directories for saving figures, caching files and storing datasets.

settings.figdir	Directory for saving figures (default './figures/').
settings.cachedir	Directory for cache files (default './cache/').
settings.datasetdir	Directory for example datasets (default './data/').
settings.file_format_figs	File format for saving figures.
settings.file_format_data	File format for saving AnnData objects.

Print versions of packages that might influence numerical results.

logging.print_header	Versions that might influence the numerical results.
logging.print_versions	Alias for print_header.