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.
Created: July 8, 2023