Print method for "nacho" object

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

data(GSE74821)
print(GSE74821)
#> List of 11
#>  $ access              : chr "IDFILE"
#>  $ housekeeping_genes  : chr [1:8] "MRPL19" "PSMC4" "SF3A1" "RPLP0" ...
#>  $ housekeeping_predict: logi FALSE
#>  $ housekeeping_norm   : logi TRUE
#>  $ normalisation_method: chr "GLM"
#>  $ remove_outliers     : logi FALSE
#>  $ n_comp              : num 10
#>  $ data_directory      : chr "~/"
#>  $ pc_sum              :'data.frame':	10 obs. of  4 variables:
#>  $ nacho               :Classes ‘data.table’ and 'data.frame':	3456 obs. of  86 variables:
#>   ..- attr(*, "sorted")= chr "IDFILE"
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>  $ outliers_thresholds :List of 6
#>  - attr(*, "RCC_type")= chr "n1"
#>  - attr(*, "class")= chr "nacho"