In outputdir now, we have four output files.
- *_recon.csv: Imputed gene expression matrix. Row as gene, col as cell. First row as gene name, First col as the cell name.
- *_embedding.csv: Learned embedding (features) for clustering. Row as cell, col as embeddings. First row as the embedding names (no means). First col as the cell name.
- *_graph.csv: Learned graph edges of the cell graph in tuples: nodeA,nodeB,weights. First row as the name.
- *_results.txt: Identified cell types. First row as the name.
For a complete list of options provided by scGNN:
python scGNN.py --help