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/', cache_compression='lzf', 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, n_pcs=50)

Config manager for scanpy.

Attributes

autosave	Automatically save figures in figdir (default False).
autoshow	Automatically show figures if autosave == False (default True).
cache_compression	Compression for sc.read(..., cache=True) (default 'lzf').
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	Maximum 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.