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.