spatialtis_core.spatial_de.som_de
Contents
spatialtis_core.spatial_de.som_de
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Module Contents#
- spatialtis_core.spatial_de.som_de.somde(exp: pandas.DataFrame, coord: Union[List, numpy.ndarray], k: int = 20, alpha: float = 0.5, epoch: int = 100, pval: float = 0.05, qval: float = 0.05) numpy.ndarray #
A wrapper for somde, a method to identify spatial variable genes
Github: SOMDE
- Parameters
exp – A dataframe, gene name as index, spatial points as columns
coord – N*2 array of coordination
k – Number of SOM nodes
alpha – Parameters for generate pseudo gene expression
epoch – Number of epoch
qval – Threshold for pval
pval – Threshold for pval