ggseg3d: Plot brain segmentations with plotly

Source: R/ggseg3d-package.R, R/ggseg3d.R

Plotting results from analyses done on data derived from brain segmentations is a common need, but may be quite laborious. Results from such analyses are usually easier to interpret if the plot can mimmick the shape and position in the brain it represents.

ggseg3d plots and returns a plotly mesh3d object.

ggseg3d(
  .data = NULL,
  atlas = "dk_3d",
  surface = "LCBC",
  hemisphere = c("right", "subcort"),
  label = "region",
  text = NULL,
  colour = "colour",
  palette = NULL,
  na.colour = "darkgrey",
  na.alpha = 1,
  show.legend = TRUE,
  options.legend = NULL,
  ...
)

Arguments

.data

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

Either a string with the name of a 3d atlas to use.
surface

String. Which surface to plot. Either "pial","white", or "inflated"[default]
hemisphere

String. Hemisphere to plot. Either "left" or "right"[default], can also be "subcort".
label

String. Quoted name of column in atlas/data that should be used to name traces
text

String. Quoted name of column in atlas/data that should be added as extra information in the hover text.
colour

String. Quoted name of column from which colour should be supplied
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.
show.legend

Logical. Toggle legend if colour is numeric.
options.legend

list of layout changes to colour bar
...

additional arguments to add_trace

Available surfaces:

  • `inflated:` Fully inflated surface

  • `semi-inflated:` Semi-inflated surface

  • `white:` white matter surface

Value

a plotly tri-surface mesh plot

Details

This package contains data from various brain parcellations, with convenient functions to inspect the results directly on a brain-plot wither with plotly in 3d meshes.

See also

Useful links:

plot_ly, add_trace, layout, the plotly package

Author

Maintainer: Athanasia Mo Mowinckel a.m.mowinckel@psykologi.uio.no (ORCID)

Authors:

Athanasia Mowinckel and Didac Piñeiro

Examples

ggseg3d()
ggseg3d(hemisphere = "left")
ggseg3d(surface = "inflated")
ggseg3d(show.legend = FALSE)