Arranging brain views

A brain atlas typically has several views – lateral and medial for cortical atlases, or axial, coronal, and sagittal slices for subcortical and tract atlases. position_brain() controls how those views are arranged in the final plot.

The function works differently depending on the atlas type, so this vignette covers cortical and subcortical/tract atlases separately.

Cortical atlases

Cortical atlases like dk have two layout dimensions: hemi (left or right) and view (lateral, medial, etc.). The formula syntax mirrors facet_grid() – left side is rows, right side is columns:

ggplot() +
  geom_brain(
    atlas = dk(),
    position = position_brain(hemi ~ view),
    show.legend = FALSE
  ) +
  theme_void()

Cortical atlas with hemispheres as rows and views as columns.

Flip the formula to transpose the layout:

ggplot() +
  geom_brain(
    atlas = dk(),
    position = position_brain(view ~ hemi),
    show.legend = FALSE
  ) +
  theme_void()

Transposed layout with views as rows and hemispheres as columns.

Stacking all views

Use . with + to collapse everything into a single row or column. This is handy for compact figures:

ggplot() +
  geom_brain(
    atlas = dk(),
    position = position_brain(. ~ hemi + view),
    show.legend = FALSE
  ) +
  theme_void()

All brain views stacked in a single row.

ggplot() +
  geom_brain(
    atlas = dk(),
    position = position_brain(hemi + view ~ .),
    show.legend = FALSE
  ) +
  theme_void()

All brain views stacked in a single column.

Subcortical and tract atlases

Subcortical atlases like aseg and tract atlases like tracula don’t have the hemisphere/view pairing that cortical atlases do. Their views are individual slices (e.g. "axial_3", "sagittal"). That opens up a different set of positioning tools.

Horizontal and vertical

The simplest options. "horizontal" is the default:

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain("horizontal"),
    show.legend = FALSE
  ) +
  theme_void()

Subcortical atlas views arranged horizontally.

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain("vertical"),
    show.legend = FALSE
  ) +
  theme_void()

Subcortical atlas views arranged vertically.

Grid layouts

When you have many views, a grid keeps things readable. Specify nrow, ncol, or both:

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain(nrow = 2),
    show.legend = FALSE
  ) +
  theme_void()

Subcortical atlas views in a two-row grid.

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain(ncol = 3),
    show.legend = FALSE
  ) +
  theme_void()

Subcortical atlas views in a three-column grid.

Picking specific views

The views parameter lets you select which views to include and in what order. Check what’s available with ggseg.formats::atlas_views():

ggseg.formats::atlas_views(aseg())
#> [1] "axial_3"   "axial_4"   "axial_5"   "axial_6"   "coronal_1" "coronal_2"
#> [7] "sagittal"

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain(
      views = c("sagittal", "axial_3", "coronal_3")
    ),
    show.legend = FALSE
  ) +
  theme_void()

A subset of subcortical views selected by name.

Combine views with nrow or ncol for a custom grid:

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain(
      views = c("sagittal", "axial_3", "axial_5", "coronal_3"),
      nrow = 2
    ),
    show.legend = FALSE
  ) +
  theme_void()

Custom two-row grid with selected subcortical views.

Grouping by slice type

The type ~ . formula groups views by their orientation – all axial slices together, all coronal slices together, and so on. The type is extracted from the view name (everything before the first underscore):

ggplot() +
  geom_brain(
    atlas = aseg(),
    position = position_brain(type ~ .),
    show.legend = FALSE
  ) +
  theme_void()

Pre-processing with reposition_brain()

If you’re using the geom_sf() workflow instead of geom_brain(), use reposition_brain() to rearrange the data before plotting. It takes the same arguments:

atlas_data <- as.data.frame(aseg())

repositioned <- reposition_brain(
  atlas_data,
  views = c("sagittal", "axial_3", "coronal_3"),
  nrow = 1
)

ggplot(repositioned) +
  geom_sf(aes(fill = region), show.legend = FALSE) +
  theme_void()

Repositioned subcortical data plotted with geom_sf().

Adding view labels

Use annotate_brain() to label each view with its name. For cortical atlases the label combines hemisphere and view (e.g. “left lateral”); for subcortical and tract atlases it uses the view name directly.

Store the position_brain() specification in an object so both layers share the same layout:

pos <- position_brain(hemi ~ view)
ggplot() +
  geom_brain(atlas = dk(), position = pos, show.legend = FALSE) +
  annotate_brain(atlas = dk(), position = pos) +
  theme_void()

Cortical atlas with view labels.

It works with any positioning — horizontal, vertical, grid, and formula layouts:

pos <- position_brain(nrow = 2)
ggplot() +
  geom_brain(atlas = aseg(), position = pos, show.legend = FALSE) +
  annotate_brain(atlas = aseg(), position = pos) +
  theme_void()

Subcortical atlas with view labels in a two-row grid.

Text appearance is customisable through standard annotate() arguments:

ggplot() +
  geom_brain(atlas = dk(), show.legend = FALSE) +
  annotate_brain(
    atlas = dk(),
    size = 2.5,
    colour = "grey50",
    fontface = "italic"
  ) +
  theme_void()

View labels with custom styling.

Quick reference

Atlas type	Options
Cortical	`hemi ~ view`, `view ~ hemi`, `. ~ hemi + view`, `hemi + view ~ .`
Subcortical / Tract	`"horizontal"`, `"vertical"`, `nrow`, `ncol`, `views`, `type ~ .`