API Reference

Complete API documentation auto-generated from code docstrings.

Main Visualization Function

vis(adata, position, color, section=None, annotations=None, continuous=None, genes=None, layer=None, height=600, mode='3D', _async_workers=2, _wait_for_all_sends=False)

Create and return a SpatialVista visualization widget.

If _wait_for_all_sends is True, the function will block until all background sends finish. Otherwise it will return the widget immediately while sends may continue in background.

Parameters:

Name	Type	Description	Default
adata	AnnData	Annotated data object containing spatial information.	required
position	str	Key in adata.obsm containing spatial coordinates.	required
color	str	Key in adata.obs for default categorical coloring.	required
section	str	Annotation key for section slicing (only relevant when mode="3D" and switching to 2D slice view in UI). Ignored when mode="2D".	None
annotations	list[str]	List of additional categorical annotation keys to export.	None
continuous	list[str]	List of continuous observation keys to export.	None
genes	list[str]	List of gene names to export.	None
layer	str	Layer to use for gene expression values. If None, uses adata.X.	None
height	int	Height of the widget in pixels.	600
mode	str	Visualization mode. "3D" for 3D point cloud, "2D" for 2D projection (z=0).	"3D"
_async_workers	int	Number of background workers for async trait sends.	2
_wait_for_all_sends	bool	Whether to wait for all background sends to complete before returning.	False

Returns:

Type	Description
SpatialVistaWidget	The configured widget ready for display.

Examples:

>>> import spatialvista as spv
>>>
>>> # Basic usage
>>> widget = spv.vis(adata, position="spatial", color="region")
>>>
>>> # With logging enabled
>>> spv.set_log_level("INFO")
>>> widget = spv.vis(adata, position="spatial", color="region")

Logging Functions

set_log_level(level='WARNING')

Set the logging level for the spatialvista package.

Parameters:

Name	Type	Description	Default
level	str	The logging level. Valid values are: - "TRACE": Most verbose, shows all messages - "DEBUG": Debug information - "INFO": General information - "SUCCESS": Success messages - "WARNING": Warning messages (default) - "ERROR": Error messages only - "CRITICAL": Critical errors only	"WARNING"

Raises:

Type	Description
ValueError	If an invalid log level is provided.

Examples:

>>> import spatialvista as spv
>>> spv.set_log_level("INFO")  # Show info and above
>>> spv.set_log_level("DEBUG")  # Show debug and above
>>> spv.set_log_level("ERROR")  # Only show errors

get_log_level()

Get the current logging level.

Returns:

Type	Description
str	The current log level (e.g., "WARNING", "INFO").

get_logger()

Get the configured logger instance.

Returns:

Type	Description
logger	The configured loguru logger instance.