Config¶

SpatialTis allows you to set global configuration, so that you don’t have to specify some parameters in every function.

To set the config:

from spatialtis import CONFIG

Here is some useful configurations you will deal with a lot, all the names are CAPITALIZED.

Options	Description	Default Value	Type
`OS`	Operating system	Detect automatically	str
`MP`	Use multi-processing	`True`	bool
`WORKING_ENV`	The current working environment	Detect automatically	str
`VERBOSE`	Control the print statement	`True`	bool
`PBAR`	Control the process bar	`True`	bool
`AUTO_SAVE`	To autosave the visualization results	`False`	bool or Path
`EXP_OBS`	The design of the experiment data	`None`	List[str]
`ROI_KEY`	The key of ROI	`None`	str

Storage keys, please explicitly specify for your own data

Options	Description	Default Value	Type
`CELL_TYPE_KEY`	Cell type key in AnnData.obs	`None`	str
`MARKER_KEY`	Marker key in AnnData.var	`marker`	str
`NEIGHBORS_KEY`	Neighbors key in AnnData.obs	`cell_neighbors`	str
`CENTROID_KEY`	Centroid key in AnnData.obs	`centroid`	str
`AREA_KEY`	Area key in AnnData.obs	`area`	str
`SHAPE_KEY`	Shape key in AnnData.obs	`cell_shape`	str
`ECCENTRICITY_KEY`	Eccentricity key in AnnData.obs	`eccentricity`	str

SpatialTis 0.3.2 documentation