Batch effect

GSG.GSG_Cluster_Comb

GSG.GSG_Cluster_Comb is a function to cluster domain using feature embedding with k-means for the mergerd data.

The input of this function is the feature embedding saved in the anndata object two_atada returned by the GSG.GSG_batch_effect_train function and the number of clustering classes you want to get, the kmeans clustering method is called in the function to perform the clustering operation on the feature embedding, and the function returns the clustering result and saves it into the anndata object.

Parameters

two_adata: anndata
       Two spatial transcriptome data.

args: argparse
      The arguments of constructing graph. 

result_file: str
       Path of storing result files.

Returns

 adatas_GSG: anndata
       Two spatial transcriptome data which removing batch effect and clustering.