Visualization And Reports

Visualization Generation

In the standard CFTK workflow, visualizations are generated from existing result files. Use vis to regenerate them without rerunning upstream processing:

cftk --config cftk_init.json vis --mode all
cftk --config cftk_init.json vis --mode power qc diff

Report Generation

Generate a HTML report:

cftk --config cftk_init.json report

Reports are written under:

<output_dir>/results/report/

Expected Outputs

vis refreshes PNG/PDF files in the process, QC, differential, fragmentomics, and MESA result directories. report writes a self-contained HTML file:

results/report/report.html

report automatically discovers the standard CFTK result directories; do not supply individual figure or metric paths. Its Workflow Summary aggregates the newest trusted status for each core-processing/QC and downstream stage from the provenance manifests, then checks the current required files. The report embeds available processing/QC, differential/DMR, occupancy, WPS, DELFI, end-motif, and MESA tables and figures. Running this command rebuilds only the HTML report and its embedded chart data; it does not rerun a completed analysis stage.

For a downstream-only project whose sample sheet points to marked BAMs from earlier CFTK projects, the report also reads the upstream processing and QC artifacts from those canonical results/1_process/3_markdup source roots automatically. The current project results take precedence, and source files are never copied or modified. This makes FastQC/MultiQC, alignment, deduplication, M-bias, QC-score, methylation-distribution, and fragment-length panels available without adding private file paths to the report command.

Every panel reflects an output that was actually found. For example, if the dinucleotide QC stage was not run, the report displays an explicit Dinucleotide QC was not produced notice and the command needed to generate it; it does not substitute a synthetic or partial plot.

The preview below is a sanitized static overview derived from the completed five-control/five-sALS technical report. It displays the discovered report sections and aggregate artifact counts without embedding patient identifiers, source paths, or the private HTML. The underlying report.html remains the authoritative interactive report and should be archived with the config, lock, command ledger, run manifest, and source result tables that produced it. This technical example is not biological or clinical validation; targeted fragmentomics panels are explicitly panel-overlap summaries, and cleavage was not run in this example. The public repository still contains a separate legacy sample_report.html demonstration; it is labeled as demo content and is not this validation result.

Sanitized static overview of the observed ten-sample technical report. Interactive charts remain interactive in report.html; this PNG is a public-safe visual index of the sections and outputs found in that report. The aggregate evidence metadata is available as JSON.