graph-structure 0.0.1

Calculate structural properties of graphs and subgraphs based on node attributes.

Graph Structure

Package focused on reading and analyzing graphs structures. It will perform a structural analysis on an undirected graph and their attribute-defined subgraphs. By providing an edge list and node attributes, it will automate the extraction of the following metrics of the graph and attribute-based subgraph:

• Number of nodes.
• Number of edges.
• Graph density.
• Number of connected components.
• Transitivity.
• Node-level characteristics:
  • Node Degree Distribution.
  • Betweenness centrality distribution.
  • Closeness centrality distribution
• Edge-level characteristics (if weighted graph):
  • Edges weight distribution
• Assortativity of the selected attribute

For the distributions, it also include descriptive statistics that summarize the central tendency, dispersion and shape of each property.

Installation

pip install graph-structure

Upgrade to a newer version using:
pip install graph-structure --upgrade

Usage

usage: graph_structure [-h] -e EDGES_FILE -n NODE_FILE -a ATTRIBUTE [-o OUTPUT_DIR] 

Structural properties analysis of graph and attribute-base subgraphs

options:
  -h, --help            show this help message and exit
  -e, --edges-file EDGES_FILE
                        Input TSV file with edges.
  -n, --node-file NODE_FILE
                        Input TSV file with node attributes.
  -a, --attribute ATTRIBUTE
                        Name of the attribute for subgraphs
  -o, --output-dir OUTPUT_DIR
                        Directory for output files.

Input format

The input formats are the same as those accepted for cytoscape to import a network and attributes from table.

1. Network Edges File

A two or three-column tab-delimited file. The header must include Source and Target (and optionally Weight).

Source	Target	Weight
node01	node03	85.71
node01	node04	90.91
node01	node06	95.24
node02	node05	90.91
node02	node09	70.42
node03	node04	67.65
node03	node06	95.0
node05	node09	94.12
node07  node08  100
node10

2. Node Attribute File

A tab-delimited file with at least two columns. The first column must be named NodeID. Subsequent columns represent the attributes used for subgraph extraction.

NodeID  GenomeID  Country
node01  ID01  Sweden
node02  ID01  Sweden
node03	ID02  USA
node04	ID03  Norway
node05	ID03  Norway
node06  ID04  Sweden
node07  ID05  Spain
node08  ID05  Spain
node09  ID06  Denmark
node10  ID07  Japan