Skip to content

Export

The Export command converts the pairwise TSV file to a dissimilarity matrix and (optionally) a newick-format file.

Usage: DBRetina export [OPTIONS]

  Export to distance matrix and tree formats.

  Export a pairwise TSV file into a distance matrix, newick-format file and
  circular dendrogram.

Options:
  -p, --pairwise PATH  pairwise TSV file  [required]
  -m, --metric TEXT    select from ['containment', 'ochiai', 'jaccard',
                       'pvalue']  [required]
  --newick             Convert the distance matrix to newick tree format
  -l, --labels TEXT    select from ['ids', 'names']  [default: names]
  --linkage TEXT       select from ['single', 'complete', 'average',
                       'weighted', 'centroid', 'median', 'ward']  [default:
                       ward]
  -o, --output TEXT    output prefix  [required]
  --help               Show this message and exit.

Command arguments

-p, --pairwise PATH pairwise TSV file [required]

The original or a filtered pairwise TSV file.

-m, --metric TEXT select from ['containment', 'ochiai', 'jaccard', 'pvalue'] [required]

The similarity metric to be utilized in the dissimilarity matrix.

--newick Convert the dissimilarity matrix to newick tree format

This will convert the dissimilarity matrix to a newick tree format.

-l, --labels TEXT select from ['ids', 'names'] [default: names]

The labels to be used in all outputs (plots, newick, dissimilarity matrix). Default is names. The option option is the IDs which are the IDs found in the {index_prefix}.namesMap file.

--linkage TEXT select from ['single', 'complete', 'average', 'weighted', 'centroid', 'median', 'ward'] [default: ward]

-o, --output TEXT output prefix [required]

The output files prefix.


Output files format

{output_prefix}_distmat.tsv

A labels tab-separated similarity matrix file.

{output_prefix}_distmat.pkl

A labels pickle similarity matrix file in Python pickle format.

{output_prefix}.newick

A newick tree file that can be used in tree visualization tools.

{output_prefix}_dendrogram.png

A circular dendrogram plot of the tree.

{output_prefix}_heatmap.png

A heatmap plot of the similarity matrix.

Image title

Image title


Last update: July 8, 2023
Created: July 8, 2023
Authors: mr-eyes