labsyspharm/mc-fastpg repository overview

docker run --rm -v "$PWD":/data labsyspharm/mc-fastpg:1.0.4 python3 /app/cluster.py \
  -i /data/unmicst-exemplar-001.csv -o /data/

usage: cluster.py [-h] -i INPUT [-o OUTPUT] [-m MARKERS] [-v] [-k NEIGHBORS]
                  [-n NUM_THREADS] [-c] [-y CONFIG] [--force-transform]
                  [--no-transform]

Cluster cell types using mcmicro marker expression data.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input CSV of mcmicro marker expression data for cells
  -o OUTPUT, --output OUTPUT
                        The directory to which output files will be saved
  -m MARKERS, --markers MARKERS
                        A text file with a marker on each line to specify
                        which markers to use for clustering
  -v, --verbose         Flag to print out progress of script
  -k NEIGHBORS, --neighbors NEIGHBORS
                        the number of nearest neighbors to use when
                        clustering. The default is 30.
  -n NUM_THREADS, --num-threads NUM_THREADS
                        the number of cpus to use during the k nearest
                        neighbors part of clustering. The default is 1.
  -c, --method          Include a column with the method name in the output
                        files.
  -y CONFIG, --config CONFIG
                        A yaml config file that states whether the input data
                        should be log/logicle transformed.
  --force-transform     Log transform the input data. If omitted, and --no-
                        transform is omitted, log transform is only performed
                        if the max value in the input data is >1000.
  --no-transform        Do not perform Log transformation on the input data.
                        If omitted, and --force-transform is omitted, log
                        transform is only performed if the max value in the
                        input data is >1000.