S3 generic that dispatches to atlas-type-specific preparation methods. Builds mesh data structures and legend data from a `ggseg_atlas`.
Usage
# S3 method for class 'cortical_atlas'
prepare_brain_meshes(
atlas,
.data = NULL,
surface = "LCBC",
hemisphere = c("right", "left"),
label_by = "region",
text_by = NULL,
colour_by = "colour",
palette = NULL,
na_colour = "darkgrey",
na_alpha = 1,
edge_by = NULL,
brain_meshes = NULL,
...
)
# S3 method for class 'subcortical_atlas'
prepare_brain_meshes(
atlas,
.data = NULL,
label_by = "region",
text_by = NULL,
colour_by = "colour",
palette = NULL,
na_colour = "darkgrey",
na_alpha = 1,
...
)
# S3 method for class 'cerebellar_atlas'
prepare_brain_meshes(
atlas,
.data = NULL,
label_by = "region",
text_by = NULL,
colour_by = "colour",
palette = NULL,
na_colour = "darkgrey",
na_alpha = 1,
surface_opacity = NULL,
...
)
# S3 method for class 'tract_atlas'
prepare_brain_meshes(
atlas,
.data = NULL,
label_by = "region",
text_by = NULL,
colour_by = "colour",
palette = NULL,
na_colour = "darkgrey",
na_alpha = 1,
tract_color = c("palette", "orientation"),
tube_radius = 2,
tube_segments = 10,
...
)
prepare_brain_meshes(atlas, ...)Arguments
- atlas
A `ggseg_atlas` object
- .data
A data.frame to use for plot aesthetics. Must include a column called "region" corresponding to regions.
- surface
Surface type: `"inflated"` (default), `"semi-inflated"`, `"white"`, `"pial"`. Use `"LCBC"` as alias for `"inflated"`.
- hemisphere
Character vector of hemispheres: `"right"`, `"left"`.
- 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.
- edge_by
Column name for region boundary edge grouping
- brain_meshes
Optional user-supplied mesh data. Passed through to [ggseg.formats::get_brain_mesh()] for format details.
- ...
Type-specific arguments passed to methods
- surface_opacity
Numeric opacity for the cerebellar surface mesh. Defaults to `0.3` when deep nuclei are present and `1` otherwise.
- tract_color
`"palette"` (default) or `"orientation"` (direction-based RGB colouring)
- tube_radius
Numeric tube radius (default 5 when `NULL`).
- tube_segments
Integer tube segment count (default 8 when `NULL`).