spatialtis.spatial_coexp#
- spatialtis.spatial_coexp(data, method='spearman', use_cell_type=False, selected_markers=None, layer_key=None, corr_thresh=0.5, export_key='spatial_coexp', **kwargs)[source]#
Identifying spatial co-expression markers using correlation
The correlation is calculated within pairs of neighbor cells
- Parameters
- dataAnnData
The AnnData to work with.
- method{‘spearman’, ‘pearson’}, default: ‘spearman’
- use_cell_typebool
Whether to use cell type information.
- selected_markerslist of str
Select your interested markers.
- corr_threshfloat, default: 0.5
The minimum correlation value to store the result.
- layer_keystr
The layer in AnnData to perform analysis.
- export_keystr
The key used to store result.
- **kwargs
Config for the analysis, for details check
spatialtis.abc.AnalysisBase
.