API Reference

Visualization Functions

Core plotting functions for 2D and 3D brain visualization

geom_brain
ggseg3d	Create an interactive 3D brain atlas visualization.

Built-in brain atlases

Functions to modify 3D plots (pipe-style)

pan_camera	Set camera position using R ggseg3d-style view names.
set_background	Set the background color of the 3D plot.
add_glassbrain	Add a transparent glass brain mesh for context.
set_legend	Configure the legend visibility.
remove_legend	Remove the legend from the plot.
set_hover	Configure hover information.

Functions for joining data with atlases

Merge user data with atlas geometry.

Functions for querying and manipulating atlases

atlas_regions	Extract unique region names from an atlas.
atlas_labels	Extract unique labels from an atlas.
atlas_views	Get available views in atlas.
atlas_palette	Get atlas color palette.
atlas_sf	Get atlas 2D geometry data.
atlas_type	Get atlas type.
atlas_region_remove	Remove regions matching a pattern.
atlas_region_keep	Keep only regions matching a pattern.
atlas_region_rename	Rename regions matching a pattern.
atlas_region_contextual	Keep region geometry but remove from core/palette.
atlas_view_remove	Remove views matching pattern from sf data.
atlas_view_keep	Keep only views matching pattern.
atlas_view_gather	Reposition views to close gaps after view removal.
atlas_view_reorder	Reorder views and reposition.
atlas_view_remove_region	Remove specific region geometry from sf data only.
atlas_view_remove_small	Remove region geometries below a minimum area threshold.
atlas_core_add	Join additional metadata columns to atlas core.

Plotnine themes for brain plots

theme_brain	Clean theme for brain plots with minimal axes.
theme_darkbrain	Dark theme for brain plots.
theme_custombrain	Customizable theme for brain plots.
theme_brain_void	Void theme with no axes, background, or grid.

Core data structures

BrainAtlas	Brain atlas container for 2D and 3D visualization.
CorticalAtlas
SubcorticalAtlas
TractAtlas