:py:mod:`spatialtis_core.spatial_de.som_de`
===========================================

.. py:module:: spatialtis_core.spatial_de.som_de


Module Contents
---------------

.. py:function:: 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

   `Publications <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab471/6308937>`_

   Github: `SOMDE <https://github.com/WhirlFirst/somde>`_

   :param exp: A dataframe, gene name as index, spatial points as columns
   :param coord: N*2 array of coordination
   :param k: Number of SOM nodes
   :param alpha: Parameters for generate pseudo gene expression
   :param epoch: Number of epoch
   :param qval: Threshold for pval
   :param pval: Threshold for pval