Example Commands

CM++

python3 -m hm01.cm 
  -i network.tsv 
  -e clustering.tsv 
  -o output.tsv 
  -c leiden 
  -g 0.5 
  -t 1log10 
  --nprocs 4 
  --quiet
python3 -m hm01.cm 
  -i network.tsv 
  -e clustering.tsv 
  -o output.tsv 
  -c ikc
  -k 10 
  -t 1log10 
  --nprocs 4 
  --quiet

CM Pipeline

{
    "title": "example",
    "name": "example",
    "input_file": "network.tsv",
    "output_dir": "samples/",
    "algorithm": "leiden",
    "params": [{
        "res": 0.5,
        "i": 2,
        "existing_clustering": "clustering.tsv"
    }],
    "stages": [
        {
            "name": "connectivity_modifier",
            "memprof": false,
            "threshold": "1log10",
            "nprocs": 1,
            "quiet": true
        }
    ]
}