print.nacho: Print method for "nacho" object

Description

This function allows to print text and figures from the results of a call to load_rcc() or normalise(). It is intended to be used in a Rmarkdown chunk.

Usage

# S3 method for nacho
print(
  x,
  colour = "CartridgeID",
  size = 0.5,
  show_legend = FALSE,
  show_outliers = TRUE,
  outliers_factor = 1,
  outliers_labels = NULL,
  echo = FALSE,
  title_level = 1,
  xaringan = FALSE,
  ...
)

Arguments

x: [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$nacho to be used as grouping colour.
size: [numeric] A numeric controlling point size (ggplot2::geom_point() or line size (ggplot2::geom_line()).
show_legend: [logical] Boolean to indicate whether the plot legends should be plotted (TRUE) or not (FALSE). Default is TRUE.
show_outliers: [logical] Boolean to indicate whether the outliers should be highlighted in red (TRUE) or not (FALSE). Default is TRUE.
outliers_factor: [numeric] Size factor for outliers compared to size. Default is 1.
outliers_labels: [character] Character to indicate which column in nacho_object$nacho should be used to be printed as the labels for outliers or not. Default is NULL.
echo: [logical] A boolean to indicate whether text and plots should be printed. Mainly for use within a Rmarkdown chunk.
title_level: [numeric] A numeric to indicate the title level to start with, using markdown style, i.e., the number of "#".
xaringan: [logical] A boolean to format output for Xaringan slides.
...: Other arguments (Not used).

Examples

Run this code


data(GSE74821)
print(GSE74821)

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