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 instance of the ScanpyConfig is available as scanpy.settings and allows configuring Scanpy.

_settings.ScanpyConfig

Config manager for scanpy.

Some selected settings are discussed in the following.

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

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

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

figdir	Directory for saving figures (default './figures/').
cachedir	Directory for cache files (default './cache/').
datasetdir	Directory for example datasets (default './data/').

The verbosity of logging output, where verbosity levels have the following meaning: 0=’error’, 1=’warning’, 2=’info’, 3=’hint’, 4=more details, 5=even more details, etc.

verbosity

Verbosity level (default warning)

Print versions of packages that might influence numerical results.

logging.print_header	Versions that might influence the numerical results.
logging.print_versions	Print versions of imported packages, OS, and jupyter environment.