Bipartite
The Bipartite command will create a bipartite graph from a pairwise TSV file between two groups files.
Usage: DBRetina bipartite [OPTIONS]
Create a bipartite connections between two group files
Options:
-p, --pairwise PATH the pairwise TSV file [required]
--group1 PATH group1 single-column supergroups file [required]
--group2 PATH group2 single-column supergroups file [required]
-m, --metric TEXT select from ['containment', 'ochiai', 'jaccard',
'pvalue'] [required]
-o, --output TEXT output file prefix [required]
--help Show this message and exit.
Command arguments
-p, --pairwise PATH the pairwise TSV file [required]
The original or a filtered pairwise TSV file.
--group1 PATH group1 single-column supergroups file [required]
A single-column file with the group1 supergroups.
--group2 PATH group2 single-column supergroups file [required]
A single-column file with the group2 supergroups.
-m, --metric TEXT select from ['containment', 'ochiai', 'jaccard', 'pvalue'] [required]
The similarity metric that will be used to create the bipartite graph.
-o, --output TEXT output prefix [required]
The output files prefix.
Output files format
{output_prefix}_bipartite_pairwise.tsv
A pairwise TSV file with the bipartite connections.
{output_prefix}_bipartite.html
An interactive bipartite graph in HTML format.
{output_prefix}_bipartite.png
A bipartite graph in PNG format.
{output_prefix}_missing_groups.txt
If there are missing groups in the group files, they will be reported in this file.
Created: July 8, 2023