In a project

To use cellmaps_vnn in a project:

import cellmaps_vnn

Example (for training):

from cellmaps_vnn.train import VNNTrain
from cellmaps_vnn.runner import CellmapsvnnRunner

train_cmd = VNNTrain(
    outdir="<output_directory>",
    inputdir="<input_directory>",
    training_data="<training_data_file>",
    gene2id="<gene2id_file>",
    cell2id="<cell2id_file>",
    mutations="<mutations_file>",
    cn_deletions="<copy_number_deletions_file>",
    cn_amplifications="<copy_number_amplifications_file>"
)

runner = CellmapsvnnRunner(
    outdir="<output_directory>",
    command=train_cmd,
    inputdir="<input_directory>"
)

runner.run()

Tutorial

Step by step tutorial on how to use Cell Maps VNN in a project is available in this Jupyter Notebook.