Angenieux: R6 Class for visualising floundeR based datasets

In sagrudd/floundeR: Toolkit For Nanopore Sequence Analysis

R6 Class for visualising floundeR based datasets

Description

This class aims to provide aplanat-like visualisation abstraction for the floundeR framework

Super class

floundeR::FloundeR -> Angenieux

Public fields

colourMap

• default colourMap for plots requiring discrete colours

Active bindings

data

A method to dump out the stored data from an Angenieux object

Methods

Public methods

• Angenieux$new()

• Angenieux$add()

• Angenieux$plot()

• Angenieux$to_file()

• Angenieux$set_title()

• Angenieux$clone()

Inherited methods

• floundeR::FloundeR$bin_data()
• floundeR::FloundeR$num_scale()
• floundeR::FloundeR$nums_scale()
• floundeR::FloundeR$print()

---

Method new()

Creates a new Angenieux object. This initialisation method performs other sanity checking of the defined file(s) and creates the required data structures.

Usage

Angenieux$new(key, value)

Arguments

key

the datatype that is being passed to the object

value

the data that is being passed to the object

Returns

A new Angenieux object.

---

Method add()

add an AngenieuxDecoration to the plot.

Usage

Angenieux$add(item)

Arguments

item

an AngenieuxDecoration

---

Method plot()

Prepare and present an Angenieux plot

Usage

Angenieux$plot(...)

Arguments

...

parameters passed on to downstream methods - please see examples for further examples as to how Angenieux plots can be customised using this approach.

---

Method to_file()

Specify that Angenieux plot should be saved to file

When working at the console an Angenieux plot may be plotted directly to the console. When preparing reports through Rmarkdown or Pkgdown a more logical saving of plots to a discrete file location may make more sense. The method is used to instruct Angenieux that the plot should be saved to a given location and with a given file format.

Usage

Angenieux$to_file(
  target_file,
  width = 18,
  height = 12,
  units = "cm",
  dpi = "print"
)

Arguments

target_file

the file with extension e.g. figure1.png

width

the width of figure to save (12 by default)

height

the height of figure to save (7.5 by default)

units

the unit to use for height and width (cm by default)

dpi

the plot resolution (print/300 by default)

Returns

the original Angenieux object (self)

---

Method set_title()

Set the title used in the given Angenieux plot

Usage

Angenieux$set_title(title)

Arguments

title

• the title to use on the plot

Returns

the original Angenieux object (self)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Angenieux$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

sagrudd/floundeR documentation built on Nov. 18, 2022, 10:31 a.m.