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Plot Glasser Atlas

Source: R/atlas_methods.R, R/glasser.R, R/print-plot-methods.R
plot-methods.Rd

Visualise a Glasser atlas object. For surface atlases (glasser_surf), renders via plot_brain(). For volumetric Glasser atlases, falls back to the base plot.atlas() method.

Volumetric slice visualisation for any atlas object. By default renders a multi-slice montage with each parcel coloured by the atlas_roi_colors() system. An orthogonal three-plane view is also available.

Usage

# S3 method for class 'atlas'
plot(
  x,
  y,
  view = c("montage", "ortho"),
  method = "rule_hcl",
  colors = NULL,
  nslices = 12L,
  ...
)

# S3 method for class 'glasser'
plot(
  x,
  y,
  vals = NULL,
  thresh = c(0, 0),
  pos = FALSE,
  palette = "cork",
  lim = NULL,
  ...
)

# S3 method for class 'surfatlas'
plot(x, y, vals = NULL, views = c("lateral", "medial"), ...)

Arguments

x

An atlas object (atlas, glasser, schaefer, etc.)

y

Ignored (required for S3 consistency)

view

Character; "montage" (default) for a multi-slice montage or "ortho" for three orthogonal planes.

method

Colour algorithm passed to atlas_roi_colors(). One of "rule_hcl" (default), "network_harmony", "maximin_view", or "embedding".

colors

Optional pre-computed colour specification: a tibble from atlas_roi_colors(), or a named character vector of hex colours keyed by region ID.

nslices

Number of slices for montage view (default 12).

...

Additional arguments passed to neuroim2::plot_montage() or neuroim2::plot_ortho().

vals

Numeric vector of values to visualize. If NULL (default), all regions will be assigned a value of 1, creating a uniform visualization

thresh

Numeric vector of length 2 for thresholding values

pos

Logical. If TRUE, uses raw values for thresholding

palette

Character. Name of scico color palette

lim

Numeric vector of length 2 for color scale limits. If NULL, will be set to range of vals

views

Character vector of views to render for surface atlases. Any combination of "lateral", "medial", "dorsal", "ventral". Default: c("lateral", "medial").

Value

A ggplot2 or ggiraph object

For view = "montage", a ggplot2 object (invisibly). For view = "ortho", a patchwork composite (if available) or a list of three ggplot2 objects.

Details

plot.surfatlas renders a cortical surface projection via plot_brain().

See also

atlas_roi_colors, ggseg_schaefer

Examples

# \donttest{
atlas <- get_aseg_atlas()
plot(atlas)

plot(atlas, view = "ortho")


plot(atlas, method = "maximin_view", nslices = 6)

# }