R6 class for a single layer of a ggbrain panel using outline geom

R6 class for a single layer of a ggbrain panel using outline geom

R6 class for a single layer of a ggbrain panel using outline geom

Value

a ggbrain_layer_outline R6 class with fields related to a brain visual layer (relates to geom_outline)

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_outline().

Super class

ggbrain::ggbrain_layer -> ggbrain_layer_outline

Active bindings

mapping

the ggplot2 aesthetic mapping between the data columns and the display

outline

controls color of outline draw around non-NA (valid) voxels

outline_scale

a scale_fill_* object containing the ggplot2 outline color scale for this layer

size

controls size of outline drawn around non-NA (valid) voxels

dil_ero

controls the number of pixels to dilate (> 0) or erode (< 0) the outline

Methods

Public methods

• ggbrain_layer_outline$new()

• ggbrain_layer_outline$clone()

Inherited methods

• ggbrain::ggbrain_layer$add_to_gg()
• ggbrain::ggbrain_layer$get_data()
• ggbrain::ggbrain_layer$is_empty()
• ggbrain::ggbrain_layer$plot()
• ggbrain::ggbrain_layer$set_breaks()
• ggbrain::ggbrain_layer$set_limits()
• ggbrain::ggbrain_layer$set_neg_breaks()
• ggbrain::ggbrain_layer$set_neg_limits()
• ggbrain::ggbrain_layer$set_pos_breaks()
• ggbrain::ggbrain_layer$set_pos_limits()

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Method new()

create a new ggbrain_layer object

Usage

ggbrain_layer_outline$new(
  name = NULL,
  definition = NULL,
  limits = NULL,
  breaks = integer_breaks(),
  show_legend = TRUE,
  interpolate = NULL,
  unify_scales = TRUE,
  alpha = NULL,
  mapping = ggplot2::aes(outline = NULL, fill = NULL),
  outline = NULL,
  outline_scale = NULL,
  size = NULL,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL,
  dil_ero = 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

a number between 0 and 1 that sets the alpha transparency of this layer. Default: 1

mapping

the aesthetic mapping of the layer data to the display. Should be an aes() object and supports outline (color of outline around clusters). Default is aes(outline=value), which maps the numeric value of the layer data to the outline color of the squares at around spatial regions. For labeled data, you might use aes(fill=<label_col_name>).

outline

A character string indicating the color used to outline all non-NA pixels in this layer. This is used in distinction to mapping=aes(outline=<variable>).

outline_scale

a ggplot scale object used for mapping the value column as the outline color for the layer.

size

controls the thickness of outlines

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

dil_ero

the number of pixels to dilate (> 0) or erode (<0) the outline.

data

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

Details

To set mapping, you must provide a ggplot2 aes() object. A geom_outline() layer requires an outline aesthetic mapping, which controls the color of outlines drawn around regions.

note that the ggbrain_layer_outline class maps onto *_fill fields

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Method clone()

The objects of this class are cloneable with this method.

Usage

ggbrain_layer_outline$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.