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

In NACHO: NanoString Quality Control Dashboard

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$nacho to be used as grouping colour.
output_file	[character] The name of the output file.
output_dir	[character] The output directory for the rendered output_file. This allows for a choice of an alternate directory to which the output file should be written (the default output directory is the working directory, i.e., .). If a path is provided with a filename in output_file the directory specified here will take precedence. Please note that any directory path provided will create any necessary directories if they do not exist.
size	[numeric] A numeric controlling point size (ggplot2::geom_point() or line size (ggplot2::geom_line()).
show_legend	[logical] Boolean to indicate whether the plot legends should be plotted (TRUE) or not (FALSE). Default is TRUE.
show_outliers	[logical] Boolean to indicate whether the outliers should be highlighted in red (TRUE) or not (FALSE). Default is TRUE.
outliers_factor	[numeric] Size factor for outliers compared to size. Default is 1.
outliers_labels	[character] Character to indicate which column in nacho_object$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 May 29, 2024, 2:05 a.m.