Usage

The cellmaps_hierarchyeval tool is designed for conducting enrichment analyses on hierarchical networks. Its objective is to show the biological significance of various terms and components (such as genes and proteins) within these networks. Terms are used from Gene Ontology (GO), CORUM, and the Human Protein Atlas (HPA).

In a project

To use cellmaps_hierarchyeval in a project:

import cellmaps_hierarchyeval

On the command line

For information invoke cellmaps_hierarchyevalcmd.py -h

Usage

cellmaps_hierarchyevalcmd.py [outdir] [--hierarchy_dir HIERARCHYDIR] [OPTIONS]

Arguments

  • outdir

    The directory where the output, including enriched hierarchies, will be written.

  • --hierarchy_dir HIERARCHYDIR

    Directory containing the generated hierarchy from cellmaps_generate_hierarchy.

  • --max_fdr

    Maximum false discovery rate for enrichment analysis. Default is 0.05.

  • --min_jaccard_index

    Minimum Jaccard index for considering an enrichment result significant. Default is 0.1.

  • --min_comp_size

    Minimum size of a term to be considered for enrichment. Default is 4.

  • --corum

    UUID for CORUM network. Default is provided.

  • --go_cc

    UUID for GO-CC network. Default is provided.

  • --hpa

    UUID for HPA network. Default is provided.

  • --ndex_server

    NDEx server to use. Default is http://www.ndexbio.org.

  • --skip_logging

    If set, disables the creation of log files.

  • --skip_term_enrichment

    If set, SKIP enrichment against networks set via –corum, –go_cc, –hpa

  • --ollama

    Path to ollama command line binary or REST service. If value starts with http it is assumed to be a REST url and all prompts will be passed to service. For REST url the suffix api/generate must be appended. Example: http://foo/api/generate. NOTE: ollama integration with this tool is EXPERIMENTAL and interface may be changed or removed in the future.

  • --ollama_user

    Username to pass as basic auth to ollama REST service

  • --ollama_password

    Password to pass via basic autho to ollama REST service

  • --ollama_prompts

    Comma delimited value of format <MODEL NAME> or <MODEL NAME>,<PROMPT> where <PROMPT> can be path to prompt file or prompt to run. For insertion of gene set please include {GENE_SET} in prompt and tell LLM to put Process: <name> on first line with name assigned to assembly and Confidence Score: <score> on 2nd line with confidence in the name given. If just <MODEL NAME> is set, then default prompt is used with model specified. NOTE: if <MODEL NAME> is set to FAKE then a completely fake agent will be used. Also note: ollama integration with this tool is EXPERIMENTAL and interface may be changed or removed in the future.

  • --provenance

    Path to file containing provenance information about input files in JSON format. This is required if inputdir does not contain ro-crate-metadata.json file.

Optional

Logging and verbosity options.

Via Docker

Example usage

TODO: Add information about example usage

Coming soon...