scanpy._settings.ScanpyConfig

class scanpy._settings.ScanpyConfig(*, verbosity='warning', plot_suffix='', file_format_data='h5ad', file_format_figs='pdf', autosave=False, autoshow=True, writedir='./write/', cachedir='./cache/', datasetdir='./data/', figdir='./figures/', max_memory=15, n_jobs=1, logfile=None, categories_to_ignore=('N/A', 'dontknow', 'no_gate', '?'), _frameon=True, _vector_friendly=False, _low_resolution_warning=True)

Config manager for scanpy.

Attributes

autosave

Automatically save figures in figdir (default False).

autoshow

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

cachedir

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

categories_to_ignore

Categories that are omitted in plotting etc.

datasetdir

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

figdir

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

file_format_data

File format for saving AnnData objects.

file_format_figs

File format for saving figures.

logfile

The open file to write logs to.

logpath

The file path logfile was set to.

max_memory

Maximal memory usage in Gigabyte.

n_jobs

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

plot_suffix

Global suffix that is appended to figure filenames.

verbosity

Verbosity level (default warning)

writedir

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

Methods

set_figure_params([scanpy, dpi, dpi_save, …])

Set resolution/size, styling and format of figures.