render: Render a HTML report of a "nacho" object

View source: R/render.R

renderR Documentation

Render a HTML report of a "nacho" object

Description

This function create a Rmarkdown script and render it as a HTML document. The HTML document is a quality-control report using all the metrics from visualise() based on recommendations from NanoString.

Usage

render(
  nacho_object,
  colour = "CartridgeID",
  output_file = "NACHO_QC.html",
  output_dir = ".",
  size = 1,
  show_legend = TRUE,
  show_outliers = TRUE,
  outliers_factor = 1,
  outliers_labels = NULL,
  clean = TRUE
)

Arguments

nacho_object

[list] A list object of class "nacho" obtained from load_rcc() or normalise().

colour

[character] Character string of the column in ssheet_csv or more generally in nacho_object$nacho to be used as grouping colour.

output_file

[character] The name of the output file.

output_dir

[character] The output directory for the rendered output_file. This allows for a choice of an alternate directory to which the output file should be written (the default output directory is the working directory, i.e., .). If a path is provided with a filename in output_file the directory specified here will take precedence. Please note that any directory path provided will create any necessary directories if they do not exist.

size

[numeric] A numeric controlling point size (ggplot2::geom_point() or #' ggbeeswarm::geom_beeswarm()) or line size (ggplot2::geom_line()).

show_legend

[logical] Boolean to indicate whether the plot legends should be plotted (TRUE) or not (FALSE). Default is TRUE.

show_outliers

[logical] Boolean to indicate whether the outliers should be highlighted in red (TRUE) or not (FALSE). Default is TRUE.

outliers_factor

[numeric] Size factor for outliers compared to size. Default is 1.

outliers_labels

[character] Character to indicate which column in nacho_object$nacho should be used to be printed as the labels for outliers or not. Default is NULL.

clean

[logical] Boolean to indicate whether the Rmd and Rdata file used to produce the HTML report are removed from output_dir. Default is TRUE.

Examples


if (interactive()) {
  data(GSE74821)
  render(GSE74821)
}


NACHO documentation built on Nov. 25, 2022, 1:05 a.m.