Skip to contents

Render the quality-control report of a nacho object

Source: R/render.R
render.Rd

Writes a quality-control report with Quarto. The report starts with a cover that gives the study details. Then comes a decision summary, with the flagged samples and notes on how the data were processed. A table gives each setting and limit, with its meaning and its source. Each plot of autoplot() and each table has a short "How to read this". A methods appendix gives the citation and the package versions.

Usage

render(
  x,
  format = c("html", "typst"),
  output_dir = ".",
  colour = "CartridgeID",
  group = NULL,
  size = 1,
  show_legend = TRUE,
  outliers_factor = 1,
  outliers_labels = NULL,
  title = NULL,
  author = NULL
)

Arguments

x

A nacho object from load_rcc() or normalise().

format

"html" (the default) for a self-contained HTML file, or "typst" for a PDF.

output_dir

The directory to write nacho-report.html or nacho-report.pdf to. It is created when it does not exist.

colour

The column of nacho_samples(x) that colours the samples.

group

The column of nacho_samples(x) with the biological groups, or NULL. With a group, the report checks whether batches and groups are confounded; see batch_diagnostics().

size

The point size.

show_legend

If FALSE, hide the colour legends.

outliers_factor

The size of flagged samples, relative to size.

outliers_labels

The column of nacho_samples(x) that labels the flagged samples, or NULL for no labels.

title

The report title. NULL or empty uses "NanoString quality-control report". A missing value (NA) is an error.

author

Who prepared the report, as one string, for example "Jane Doe, Genomics Core". NULL or empty leaves it out. A missing value (NA) is an error.

Value

The path of the report, invisibly.

Details

The report needs the Quarto command-line interface 1.9.18 or newer, and the quarto, knitr and rmarkdown packages. RStudio and Positron bundle Quarto; elsewhere, install it from https://quarto.org/docs/get-started/. The PDF goes through Typst, which Quarto bundles, so no LaTeX is needed.

The PDF is tagged and declares PDF/UA-1. When Typst compiles the PDF, it checks the PDF/UA-1 rules that it can enforce. When Quarto shows the warning "verapdf is not installed", you can ignore it: it only means that Quarto did not do the extra validation step.

Examples

if (interactive()) {
  data(GSE74821)
  render(GSE74821, output_dir = tempdir())
  render(GSE74821, format = "typst", output_dir = tempdir())
}