CLI reference

domainator matrix_report

Summarize a similarity matrix.

Reads a DataMatrix and generates a report suitable for helping with selecting edge score thresholds for similarity networks

Give at least one of these outputs: --text_out, --html_out, --json_out. - as an input or output means standard input or output, where the option says it is allowed.

Option	Value	Default	Description
-v, --verbose			show debug output, and a traceback for errors.
-q, --quiet			show errors only: no progress messages or warnings.
-i, --input	FILE	required	name of input matrix file.
-o, --text_out	FILE		Write the report as text to this file. Use - for standard output.
--html_out	FILE		Write the report as html to this file. Use - for standard output.
--json_out	FILE		Write a compact JSON summary (edge stats, connected components, split-event series) to this file. Use - for standard output.
--knn_projection			Project how many edges 'build_ssn --threshold T --mst --knn K' would keep, for every threshold T and K from 1 to 25, and add a K slider to the HTML report. Disabled by default to reduce memory use.
--merge_impact_metric	{product,min_child}	min_child	Metric used for split-event plots and tables: 'min_child' emphasizes the smaller cluster breaking away, while 'product' emphasizes balanced large splits.
--max_merge_events	INTEGER	500	Maximum number of strongest merge events to embed in the interactive HTML threshold slider and split plot. A few more may be added on top: after the strongest are taken, the strongest event in each otherwise-empty 5% band of the threshold axis is added back, so the plot never leaves a stretch of its own axis blank. Use 0 to include all merge events.
--progress			Print live progress updates to stderr during long-running matrix_report stages.
--profile_stages			Print per-stage runtime timings to stderr for profiling large matrix_report runs.

Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.