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An R6 class for constructing a ggbrain plot from a ggbrain_slices object

Source: R/ggbrain_plot.R
ggbrain_plot.Rd

An R6 class for constructing a ggbrain plot from a ggbrain_slices object

An R6 class for constructing a ggbrain plot from a ggbrain_slices object

Value

a ggbrain_plot R6 class containing fields related to a ggbrain plot object

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 ggbrain().

Active bindings

slices

a ggbrain_slices object containing all slice data for this plot

layers

a list of ggbrain_layer objects for this plot. Note that in assignment, the input can be a list of ggbrain_layer objects, or a list of lists where each inner element specifies the settings for that layer. Example: list(list(name='hello', fill_scale=scale_fill_distiller())

annotations

a list of annotations to be added to this plot

region_labels

a list of region_labels to be added to this plot

panel_settings

a list of panel settings (aesthetics) to be added to this plot

title

overall plot title, added to composite plot by patchwork::plot_annotation()

bg_color

background color of plot

text_color

the color of text use across panels (can be overridden by panel settings)

base_size

the base size of text used in ggplot theming

Methods

Public methods

Method new()

instantiate a new instance of a ggbrain_plot object

Usage

ggbrain_plot$new(
  title = NULL,
  bg_color = NULL,
  text_color = NULL,
  base_size = NULL,
  slice_data = NULL
)

Arguments

title

overall plot title

bg_color

background color of plot

text_color

text color of plot

base_size

base size of text used in ggplot theming

slice_data

a ggbrain_slices object generated by ggbrain_images$get_slices()

Method add_layers()

adds one or more ggbrain_layer objects to this plot

Usage

ggbrain_plot$add_layers(layers = NULL)

Arguments

layers

a list of ggbrain_layer objects (can also be a list that just specifies names, definitions, etc.)

Method reset_layers()

removes all existing layers from this ggbrain_plot object

Usage

ggbrain_plot$reset_layers()

Method generate_plot()

generate the plot

Usage

ggbrain_plot$generate_plot(layers = NULL, slice_indices = NULL)

Arguments

layers

a list of layers to be displayed on each panel, the order of which yields the bottom-to-to drawing order within ggplot2. Each element of layers should be a list that follows the approximate structure of the ggbrain_layer class, minimally including the layer name, which is used to lookup data of images or contrasts within the slice_data object. If NULL, all layers in the slices object will be plotted. If only a character string is passed, then those layers will be plotted with default scales.

slice_indices

An optional subset of slice indices to display from the stored slice data

Details

In addition to name, the elements of a layer can include fill_scale a ggplot2 scale object for coloring the layer. Should be a scale_fill_* object. limits the numeric limits to use for the color scale of this layer breaks the scale breaks to use for the color scale of this layer show_legend if FALSE, the color scale will not appear in the legend

Method plot()

return a plot of all panels as a patchwork object

Usage

ggbrain_plot$plot(guides = "collect")

Arguments

guides

Passes through to patchwork::plot_layout to control how legends are combined across plots. The default is "collect", which collects legends within a given nesting level (removes duplicates).

Method clone()

The objects of this class are cloneable with this method.

Usage

ggbrain_plot$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.