spatialtis.abc.AnalysisBase#
- class spatialtis.abc.AnalysisBase(data, method=None, exp_obs=None, roi_key=None, export_key=None, cell_type_key=None, centroid_key=None, shape_key=None, marker_key=None, mp=None, display_name=None, verbose=True)[source]#
The base class for all analysis function
All parameters apply in this class can be used in analysis
- Parameters
- dataAnnData
The AnnData to work with.
- methodstr, default: None
The method used in the run of the analysis.
- export_keystr
The key used to store result.
- display_namestr, default: None
The name use to display the name of analysis.
- mpbool, default: Config.mp
Enable parallel processing, no effect since v0.5.0.
- exp_obsstr or list of str, default:
Config.exp_obs The columns in .obs that tells how your experiments organized. This will temporarily overwrite the global config.
- roi_keystr, default:
Config.roi_key The columns in .obs that specific ROI.This will temporarily overwrite the global config.
- cell_type_keystr, default:
Config.cell_type_key The column in .obs to store cell types.This will temporarily overwrite the global config.
- centroid_keystr or list of str, default:
Config.centroid_key The column in .obs or .obsm to store centroid. This will temporarily overwrite the global config.
- shape_keystr, default:
Config.shape_key The column in .var to store cell shape in wkt format. This will temporarily overwrite the global config.
- marker_keystr, default:
Config.marker_key The column in .var to store marker names.By default will read from the index of .var. This will temporarily overwrite the global config.
Methods
iter_roi([fields, filter_rois, sort, desc, ...])A generator to iterate ROI
- iter_roi(fields=None, filter_rois=None, sort=False, desc=None, disable_pbar=None, selected_markers=None, layer_key=None, dtype=None)[source]#
A generator to iterate ROI
- Parameters
- fieldslist of str, {‘centroid’, ‘exp’, ‘neighbors’, ‘cell_type’, ‘shape’, ‘label’, ‘index’}
What fields to retrieve when iterate ROI.
- filter_roislist of str
The roi to be filtered.
- sortbool
Whether to sort ROI.
- descstr
The description in the progress bar.
- disable_pbarbool
Whether to disable progress bar.
- selected_markerslist of str
The list of markers to be selected.
- layer_keystr
The layer to use for expression.
- dtype
The datatype.