Usage

The tool cellmaps_ppi_embeddingcmd.py provides functionalities for embedding protein-protein interactions (PPIs). By default, it employs the Node2Vec algorithm for generating embeddings but can also produce fake embeddings for testing purposes.

In a project

To use cellmaps_ppi_embedding in a project:

import cellmaps_ppi_embedding

On the command line

For information invoke cellmaps_ppi_embeddingcmd.py -h

Usage

cellmaps_ppi_embeddingcmd.py [outdir] [--inputdir PPIDOWNLOADER_OUT_DIR] [OPTIONS]

Arguments

• outdir

  The directory where the output will be written to.

Required

• --inputdir:

  Directory with the ppi_edgelist.tsv file. Output of the cellmaps_ppidownloader package.

Optional

• --dimensions:

  The size of the embedding to generate. Default value is 1024.

• --walk_length:

  The length of the walk for Node2Vec. Default is 80.

• --num_walks:

  The number of walks for Node2Vec. Default is 10.

• --workers:

  The number of worker threads to use. Default is 8.

• --p:

  The p value to pass to Node2Vec. Default is 2.

• --q:

  The q value to pass to Node2Vec. Default is 1.

• --fake_embedder:

  If set, the script will generate a fake embedding.

• --skip_logging:

  If set, certain log files will not be created.

• --logconf:

  Path to the python logging configuration file.

• -v or --verbose:

  Increases verbosity of the logger to standard error for log messages in the module. -v sets logging to ERROR, -vv to WARNING, -vvv to INFO, -vvvv to DEBUG, and -vvvvv to NOTSET.

• --version:

  Displays the version of the script.

Example usage

The output directory for the PPI download is required (see Cell Maps PPI Downloader).

cellmaps_ppi_embeddingcmd.py ./cellmaps_ppi_embedding_outdir --inputdir ./cellmaps_ppidownloader_outdir

Via Docker

Example usage

Coming soon...