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
a ggbrain_plot R6 class containing fields related to a ggbrain plot object
slicesa ggbrain_slices object containing all slice data for this plot
layersa 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())
annotationsa list of annotations to be added to this plot
region_labelsa list of region_labels to be added to this plot
panel_settingsa list of panel settings (aesthetics) to be added to this plot
titleoverall plot title, added to composite plot by patchwork::plot_annotation()
bg_colorbackground color of plot
text_colorthe color of text use across panels (can be overridden by panel settings)
base_sizethe base size of text used in ggplot theming
new()instantiate a new instance of a ggbrain_plot object
ggbrain_plot$new(
title = NULL,
bg_color = NULL,
text_color = NULL,
base_size = NULL,
slice_data = NULL
)titleoverall plot title
bg_colorbackground color of plot
text_colortext color of plot
base_sizebase size of text used in ggplot theming
slice_dataa ggbrain_slices object generated by ggbrain_images$get_slices()
add_layers()adds one or more ggbrain_layer objects to this plot
ggbrain_plot$add_layers(layers = NULL)layersa list of ggbrain_layer objects (can also be a list that just specifies names, definitions, etc.)
reset_layers()removes all existing layers from this ggbrain_plot object
ggbrain_plot$reset_layers()
generate_plot()generate the plot
ggbrain_plot$generate_plot(layers = NULL, slice_indices = NULL)layersa list of layers to be displayed on each panel, the order of which yields the
bottom-to-to drawing order within ggplot2. Each element of layers should be a list
that follows the approximate structure of the ggbrain_layer class, minimally including
the layer name, which is used to lookup data of images or contrasts within the
slice_data object. If NULL, all layers in the slices object will be plotted. If only
a character string is passed, then those layers will be plotted with default scales.
slice_indicesAn optional subset of slice indices to display from the stored slice data
In addition to name, the elements of a layer can include
fill_scale a ggplot2 scale object for coloring the layer. Should be a scale_fill_* object.
limits the numeric limits to use for the color scale of this layer
breaks the scale breaks to use for the color scale of this layer
show_legend if FALSE, the color scale will not appear in the legend
plot()return a plot of all panels as a patchwork object
ggbrain_plot$plot(guides = "collect", ...)guidesPasses 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).
...additional arguments. Not used currently
clone()The objects of this class are cloneable with this method.
ggbrain_plot$clone(deep = FALSE)deepWhether to make a deep clone.
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().