omicverse.bulk.pyPPI

omicverse.bulk.pyPPI#

class omicverse.bulk.pyPPI(gene, species, gene_type_dict, gene_color_dict, score=0.4)[source]#

Protein-protein interaction (PPI) analysis wrapper based on STRING.

Parameters:

  • gene (list) – Gene symbols used as seed nodes for building the interaction network.

  • species (int) – NCBI taxonomy id (e.g., 9606 for human).

  • gene_type_dict (dict) – Mapping from gene symbol to category/type used in node styling.

  • gene_color_dict (dict) – Mapping from gene symbol to display color.

  • score (float, default=0.4) – Minimum confidence score for retaining interactions.

__init__(gene, species, gene_type_dict, gene_color_dict, score=0.4)[source]#

Initialize protein-protein interaction analysis.

Parameters:

  • gene (list) – List of gene names for PPI analysis

  • species (int) – NCBI taxon identifiers (e.g. Human is 9606, see STRING organisms)

  • gene_type_dict (dict) – Dictionary mapping gene names to gene types

  • gene_color_dict (dict) – Dictionary mapping gene names to colors for visualization

  • score (float (default: 0.4)) – Threshold for protein interaction confidence (default: 0.4)

Methods

__init__(gene, species, gene_type_dict, ...)

Initialize protein-protein interaction analysis.

interaction_analysis()

Perform protein-protein interaction analysis.

plot_network(**kwargs)

Plot protein-protein interaction network.
Contents