Render brain atlas with rgl

Creates an rgl 3D scene from a brain atlas. Uses the same atlas preparation pipeline as [ggseg3d()] but outputs to rgl instead of htmlwidgets. The resulting scene can be piped into [pan_camera()], [add_glassbrain()], and [set_background()], then rendered with rayshader's `render_highquality()` or captured with `rgl::snapshot3d()`.

Usage

ggsegray(
  .data = NULL,
  atlas = dk(),
  label_by = "region",
  text_by = NULL,
  colour_by = "colour",
  palette = NULL,
  na_colour = "darkgrey",
  na_alpha = 1,
  material = list(),
  ...,
  label = deprecated(),
  text = deprecated(),
  colour = deprecated()
)

Arguments

.data

A data.frame to use for plot aesthetics. Must include a column called "region" corresponding to regions.

atlas

A `ggseg_atlas` object containing 3D vertex mappings, or a string naming an atlas function (deprecated).

label_by

String. Column name used as hover label for each region.

text_by

String. Column name for extra hover text shown below the region label.

colour_by

String. Column name mapped to mesh colours.

palette

String. Vector of colour names or HEX colours. Can also be a named numeric vector, with colours as names, and breakpoint for that colour as the value

na_colour

String. Either name, hex of RGB for colour of NA in colour.

na_alpha

Numeric. A number between 0 and 1 to control transparency of NA-regions.

material

Named list of rgl material properties passed to [rgl::tmesh3d()]. Controls how the mesh surface is shaded.

...

Type-specific arguments passed to the atlas method. See section **Type-specific arguments** below.

label, text, colour

`r lifecycle::badge("deprecated")` Use `label_by`, `text_by`, and `colour_by` instead.

Value

An object of class `ggsegray` (invisibly), which wraps the rgl device ID. Pipe into [pan_camera()], [add_glassbrain()], or [set_background()] to modify the scene.

Material properties

Useful material list entries:

`specular`

`"black"` (matte) or `"white"` (glossy).

`shininess`

Specular exponent. Higher = tighter highlights.

`lit`

`FALSE` disables lighting.

`alpha`

Transparency, 0 (invisible) to 1 (opaque).

`smooth`

`TRUE` for Gouraud shading, `FALSE` for flat.

See [rgl::material3d()] for the full list.

Type-specific arguments

Cortical atlases (`cortical_atlas`):

`surface`

Surface type: `"LCBC"` (default, alias for inflated), `"inflated"`, `"semi-inflated"`, `"white"`, `"pial"`.

`hemisphere`

Character vector of hemispheres: `"right"`, `"left"`.

`edge_by`

Column name for region boundary edges.

`brain_meshes`

Custom brain mesh data.

Tract atlases (`tract_atlas`):

`tract_color`

`"palette"` (default) or `"orientation"` (direction-based RGB).

`tube_radius`

Tube radius (numeric, default 5).

`tube_segments`

Tube segment count (integer, default 8).

Examples

if (FALSE) { # \dontrun{
ggsegray(hemisphere = "left") |>
  pan_camera("left lateral")

ggsegray(atlas = aseg()) |>
  add_glassbrain(opacity = 0.15) |>
  pan_camera("right lateral") |>
  set_background("black")
} # }