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	Allows users to customize settings for the scanpy package.
settings.override	Provides local override via keyword arguments as a context manager.

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
settings.autosave

IO related settings for saving figures, caching files and storing datasets.

settings.figdir
settings.cachedir
settings.datasetdir
settings.file_format_figs
settings.file_format_data

Print versions of packages that might influence numerical results.

logging.print_header

Versions that might influence the numerical results.