Base¶
AnalysisBase¶
-
class
spatialtis.abc.AnalysisBase(data, task_name=None, method=None, exp_obs=None, export=None, export_key=None, mp=None, cell_type_key=None, centroid_key=None, area_key=None, shape_key=None, eccentricity_key=None, marker_key=None, neighbors_key=None)[source]¶ The base class for all analysis function
All parameters apply in this class can be used in analysis
- Parameters
data (anndata._core.anndata.AnnData) – AnnData object to perform analysis
task_name (str) – The name of the analysis
method (Optional[str]) – The method used in the run of the analysis
exp_obs (List[str]) – list, How your experiments data grouped, (Default: spatialtis.CONFIG.EXP_OBS)
export (bool) – bool, Whether export the result to AnnData.uns
export_key (str) – str, The name of key used to stored the exported result
mp (bool) – bool, Whether to enable parallel processing (Default: spatialtis.CONFIG.MULTI_PROCESSING)
cell_type_key (str) – The key to store cell types in AnnData.obs (Default: spatialtis.CONFIG.CELL_TYPE_KEY)
centroid_key (str) – The key to store cell centroid in AnnData.obs (Default: spatialtis.CONFIG.CENTROID_KEY)
area_key (str) – The key to store cell area in AnnData.obs (Default: spatialtis.CONFIG.AREA_KEY)
shape_key (str) – The key to store cell shape in AnnData.obs (Default: spatialtis.CONFIG.SHAPE_KEY)
eccentricity_key (str) – The key to store cell eccentricity in AnnData.obs (Default: spatialtis.CONFIG.ECCENTRICITY_KEY)
marker_key (str) – The key to store markers in AnnData.var (Default: spatialtis.CONFIG.MARKER_KEY)
neighbors_key (str) – The key to store cell neighbors in AnnData.obs
-
result¶ To get the results
-
method¶ The method used for the analysis, might be empty
- Type
Optional[str]