scanpy.settings.override

settings.override(*, verbosity=<no change>, logfile=<no change>, N_PCS=<no change>, plot_suffix=<no change>, file_format_data=<no change>, file_format_figs=<no change>, autosave=<no change>, autoshow=<no change>, writedir=<no change>, cachedir=<no change>, datasetdir=<no change>, figdir=<no change>, cache_compression=<no change>, max_memory=<no change>, n_jobs=<no change>, categories_to_ignore=<no change>)

Provides local override via keyword arguments as a context manager.

Parameters:

preset Preset (default: <no change>)

Preset to use.

verbosity Verbosity (default: <no change>)

Verbosity level (default Verbosity.warning).

logfile Writer[str] (default: <no change>)

The open file to write logs to.

Set it to a Path or str to open a new one. By default uses sys.stdout in jupyter notebooks and sys.stderr otherwise.

N_PCS int (default: <no change>)

Default number of principal components to use.

plot_suffix str (default: <no change>)

Global suffix that is appended to figure filenames.

file_format_data Literal['h5ad', 'zarr'] (default: <no change>)

File format for saving AnnData objects.

file_format_figs str (default: <no change>)

File format for saving figures.

For example 'png', 'pdf' or 'svg'. Many other formats work as well (see matplotlib.pyplot.savefig()).

autosave bool (default: <no change>)

Automatically save figures in figdir (default False).

Do not show plots/figures interactively.

autoshow bool (default: <no change>)

Automatically show figures if autosave == False (default True).

There is no need to call the matplotlib pl.show() in this case.

writedir Path (default: <no change>)

Directory where the function scanpy.write writes to by default.

cachedir Path (default: <no change>)

Directory for cache files (default './cache/').

datasetdir Path (default: <no change>)

Directory for example datasets (default './data/').

figdir Path (default: <no change>)

Directory for autosaveing figures (default './figures/').

cache_compression Literal['lzf', 'gzip'] | None (default: <no change>)

Compression for sc.read(..., cache=True) (default 'lzf').

max_memory float (default: <no change>)

Maximum memory usage in Gigabyte.

Is currently not well respected…

n_jobs int (default: <no change>)

Default number of jobs/ CPUs to use for parallel computing.

Set to -1 in order to use all available cores. Not all algorithms support special behavior for numbers < -1, so make sure to leave this setting as >= -1.

Changed in version 1.13.0: The default changed from 1 to 4.

categories_to_ignore Container[str] (default: <no change>)

Categories that are omitted in plotting etc.

Return type:

AbstractContextManager[None]