geneGATer.tl.getComGenes#
- geneGATer.tl.getComGenes(adata, raw_cluster, tresh=0, groupby='cluster', plot=False, verbosse=True, library_key='sample_name')#
Extract communication metagenes.
- Parameters
adata (
AnnData) – The AnnData object to preprocess.
- raw_cluster
List of raw_cluster for each spot, e.g. result of gt.pp.pre_clustering.
- tresh
Threshold for the metagene detection, e.g. how many neighbouring spots should be included (the higher the less are included).
- groupby
Key for the clustering in adata.obs.
- plot
True or false if you want progress plots of the metagene iterations.
- verbosse
True or false if you want error messages printed.
- library_key
Key for donor names.
- Returns
Dict of mulitple output parameters:
- out[0]
Number of spots above the median metagene expression for each cluster/cluster combination.
- out[1]
Number of spots above the minimum metagene expression for each cluster/cluster combination.
- out[2][“cluster_i”]
Metagene expression for cluster_i and all other cluster combinations.
- out[3][“cluster_i”]
Genes of metagenes for cluster_i and all other cluster combinations.
- out[4]
All found genes in metagenes.