Write a single self-contained HTML report of everything a run produced

Presents the outputs in the order the documentation says they must be read, because each stage can invalidate the ones after it. Sections whose files are absent are omitted rather than shown empty.

Usage

write_run_report(
  outdir,
  opt = NULL,
  verdicts = NULL,
  failure = NULL,
  images = NULL
)

Arguments

outdir: the results directory, which is also where the report is written
opt: parsed options, used for the header
verdicts: per-sample staining verdicts, used for the summary banner
failure: a condition or message; when given, the report is written as the record of a failed run rather than a completed one.
images: "embed" to carry every figure inside the file (the default), or "link" to reference the PNGs beside it, which makes a report of a few megabytes that shows its figures only while it stays in the results directory. Defaults to opt$report_images, then to getOption("cyRAVEN.report_images", "embed").

Value

the path, invisibly, or NULL when there is nothing to report

Details

The file references nothing: every figure is embedded at full resolution as a data URI and every table as JSON, so the report can be moved, emailed or archived on its own. Figures can be zoomed and downloaded at full resolution; tables can be searched, sorted, paged at 10/50/100/all rows and exported to CSV.

When failure is supplied the same report is written for a run that stopped early, with a diagnosis section first and every output produced up to the failure embedded below it. The partial output is usually where the evidence is, so it is kept rather than discarded.