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.

Presets allow to set the behavior of many scanpy functions at once:

Preset

Presets for scanpy.settings.preset.

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).

IO related settings 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.