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R6 class for a single layer of a ggbrain panel

Source: R/ggbrain_layer.R
ggbrain_layer.Rd

R6 class for a single layer of a ggbrain panel

R6 class for a single layer of a ggbrain panel

Value

a ggbrain_layer R6 class containing fields related to a visual layer on the ggbrain plot

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at geom_brain() and geom_outline().

Active bindings

name

the name of this layer, used for referencing in layer and panel modifications

all_na

whether all values for this layer are NA in the data field

definition

a character string specifying the image name or contrast that defines this layer

source

a character string specifying the layer source within a relevant ggbrain_slices object. This is used to lookup the right layer information when combining slices and layers together Note that multiple layers can potentially have the same source, which is why a 1:1 mapping to name does not work

data

the data.frame containing relevant data for this layer.

show_legend

a logical indicating whether to show or hide the fill/color scale

unify_scales

a logical indicating whether to unify scale limits and levels when this layer is added across many panels

bisided

read-only access to whether this layer uses a bisided color scale

categorical_fill

read-only access to whether this layer has a categorical fill scale

fill_column

read-only access to layer fill column

fill_scale

a scale_fill_* object containing the ggplot2 fill scale for this layer

alpha

sets the alpha transparency of this layer.

blur_edge

controls the standard deviation (sigma) of a Gaussian blur applied to the layer at the edge

trim_threads

iteratively trim any pixels that have fewer than this number of neighboring pixels

fill_holes

controls the size of holes to be filled for display (in pixels)

remove_specks

controls the size of specks to be removed (in pixels)

Methods

Public methods

Method new()

create a new ggbrain_layer object

Usage

ggbrain_layer$new(
  name = NULL,
  definition = NULL,
  limits = NULL,
  breaks = integer_breaks(),
  show_legend = TRUE,
  interpolate = NULL,
  unify_scales = TRUE,
  alpha = NULL,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL,
  data = NULL
)

Arguments

name

the name of this layer, used for referencing in layer and panel modifications

definition

an optional character string defining the image or contrast that should be used to lookup data from a ggbrain_slices object. This is mostly used internally by the ggbrain + syntax to allow layers to be defined without data in advance of the plot.

limits

if provided, sets the upper and lower bounds on the scale

breaks

if provided, a function to draw the breaks on the color scale

show_legend

if TRUE, show the scale on the plot legend

interpolate

passes to geom_raster and controls whether the fill is interpolated over continuous space

unify_scales

if TRUE, when this layer is reused across panels, unify the scales to match

alpha

fixed alpha transparency of this layer (use mapping for alpha mapping`)

blur_edge

the standard deviation (sigma) of a Gaussian kernel applied to the edge of this layer to smooth it. This makes the layer less jagged in appearance and is akin to antialiasing.

fill_holes

the size of holes (in pixels) inside clusters to be filled by nearest neighbor imputation prior to display

remove_specks

the size of specks (in pixels) to be removed from each slice prior to display

trim_threads

the minimum number of neighboring pixels (including diagonals) that must be present to keep a pixel

data

the data.frame containing image data for this layer. Must contain "dim1", "dim2", and "value" as columns

Method set_limits()

set the limits for this layer's scale

Usage

ggbrain_layer$set_limits(limits)

Arguments

limits

a 2-element numeric vector setting the lower and upper limits on the layer's scale

Method set_pos_limits()

set the limits for this layer's positive scale (only relevant to bisided)

Usage

ggbrain_layer$set_pos_limits(limits)

Arguments

limits

a 2-element numeric vector setting the lower and upper limits on the layer's positive scale

Method set_neg_limits()

set the limits for this layer's positive scale (only relevant to bisided)

Usage

ggbrain_layer$set_neg_limits(limits)

Arguments

limits

a 2-element numeric vector setting the lower and upper limits on the layer's positive scale

Method set_breaks()

set the breaks element of this layer's scale

Usage

ggbrain_layer$set_breaks(breaks)

Arguments

breaks

a function used to label the breaks

Method set_pos_breaks()

set the breaks element of this layer's positive scale (only relevant to bisided)

Usage

ggbrain_layer$set_pos_breaks(breaks)

Arguments

breaks

a function used to label the positive breaks

Method set_neg_breaks()

set the breaks element of this layer's negative scale (only relevant to bisided)

Usage

ggbrain_layer$set_neg_breaks(breaks)

Arguments

breaks

a function used to label the negative breaks

Method plot()

plot this layer alone (mostly for debugging)

Usage

ggbrain_layer$plot()

Method add_to_gg()

method to add this layer to an existing ggplot object

Usage

ggbrain_layer$add_to_gg(base_gg)

Arguments

base_gg

the ggplot object to which we add the layer

Method get_data()

return the data.frame associated with this layer

Usage

ggbrain_layer$get_data(add_layer_name = FALSE)

Arguments

add_layer_name

if TRUE, adds a layer_name column to the data.frame for record-keeping. Default: FALSE.

Method is_empty()

returns TRUE if all values are NA or if the data has 0 rows

Usage

ggbrain_layer$is_empty()

Method clone()

The objects of this class are cloneable with this method.

Usage

ggbrain_layer$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.