Network Info

Before running any geneset-network analysis is a good practice to extract basic information on the network and the geneset or to visualise the network. We provide a function to obtain the network summary ( or the summary of a single genesets) and another utility to write an annotated graphml file ( visualise it on Cytoscape ).

Network Properties

network-summary saves the principal info of a graph:

• network properties
• degree distribution
• connected components diagnostic

If a geneset/setname is passed to the function, the properties of the subgraph are evaluated

pygna network-summary [-h] [-g GENESET_INPUT_FILE] [-s SETNAME] network-file text-output degree-figure-file c-components-figure-file

positional arguments:
  network-file          network file
  text-output           output text file for the summary
  degree-figure-file    pdf or png file for the degree distribution
  c-components-figure-file
                        pdf or png file for the connected components distribution

optional arguments:
  -h, --help            show this help message and exit
  -g GENESET_INPUT_FILE, --geneset-input-file GENESET_INPUT_FILE
                        geneset file (default: -)
  -s SETNAME, --setname SETNAME
                        specify a single geneset (default: -)

Cytoscape visualisation

network-graphml generates a graphml file with nodes annotation. Given a geneset, with k setnames, each node has k False/True annotations for each set.

Warning: without minimal, this function saves the full network. The minimal graph saves only the nodes in the geneset and those that connect them with a shortest path.

usage: pygna network-graphml [-h] [-s SETNAME] [--giant-component-only] [-m] network-file geneset-file output-file

positional arguments:
  network-file          network file
  geneset-file          geneset file
  output-file           graphml file for network for visualisation

optional arguments:
  -h, --help            show this help message and exit
  -s SETNAME, --setname SETNAME
                        set name (default: -)
  --giant-component-only
                        saves only the giant component of the network (default: True)
  -m, --minimal         saves only the minimal graph (default: False)

Connected components

get-connected-components evaluate all the connected components in the subgraph pf the network with a given setname. Multiple setnames can be passed to this function to analyze all of them in a run. The file produces a GMT output and optionally a plot of the subnetwork with the connected components analysed.

Please notice that to convert the entrezID into Symbols, a stable internet connection is required

usage: pygna get-connected-components [-h] [--geneset-file GENESET_FILE]
                                    [-s SETNAME] [--graphml GRAPHML]
                                    [-t THRESHOLD] [-c]
                                    network-file output-gmt name

    This function evaluate all the connected components in the subgraph pf the network with a given setname.
    Multiple setnames can be passed to this function to analyze all of them in a run.
    The file produces a GMT output and optionally a plot of the subnetwork with the connected components analysed.
    Please notice that to convert the entrezID into Symbols, a stable internet connection is required


positional arguments:
network-file          network tsv file
output-gmt            The output file name (should be gmt)
name                  pass a name for the putput gmt terms

optional arguments:
-h, --help            show this help message and exit
--geneset-file GENESET_FILE
                        GMT of the geneset file, is a file is passed please
                        add the setname (default: -)
-s SETNAME, --setname SETNAME
                        The setname to analyse (default: -)
--graphml GRAPHML     Pass a graphml filename to show the results on
                        Cytoscape (default: -)
-t THRESHOLD, --threshold THRESHOLD
                        ignores all CC smaller than this value (default: 1)
-c, --convert-entrez  pass flag to convert EntrezID->Symbol (default: False)