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Brain Montage

Source: R/minc_vis3D.R
obj_montage.Rd

Plot the left and right hemispheres of brain colourized by two colour maps with a colour bar in the middle

Usage

obj_montage(
  left_obj,
  right_obj,
  left_map,
  right_map,
  output = NULL,
  colour_map,
  colour_range = NULL,
  colour_default = "grey",
  colour_bar = TRUE,
  labels = FALSE,
  palette = heat.colors(255),
  symmetric = FALSE,
  par = list(),
  vertical = TRUE,
  layout = if (vertical) function() rgl::mfrow3d(3, 2, byrow = TRUE) else function()
    rgl::mfrow3d(2, 3, byrow = FALSE),
  ...,
  plot_corners = c(100, 100, 900, 900),
  zoom = 1,
  add_normals = TRUE,
  colour_title = "",
  close_on_output = TRUE
)

Arguments

left_obj

A bic_obj probably created by read_obj with the left hemisphere of a subject's brain

right_obj

A bic_obj probably created by read_obj with the right hemisphere of a subject's brain

left_map

a colour map to apply to the left hemisphere see colour_mesh for details

right_map

a colour map to apply to the right hemisphere see colour_mesh for details

output

Either NULL or a file path to write the snapshot.

colour_map

either a vector with a label/measure/statistic for every vertex or a character file path pointing to a file with such a vector in a rowwise format.

colour_range

a two element numeric vector indicating the min and max values of allowable labels/measures/statistics to be includedon the surface

colour_default

The colour given to vertices excluded by colour_range

colour_bar

Whether or not to draw a colour bar in the figure

labels

Whether or not the colour_map is a set of discrete labels

palette

A palette, AKA look-up-table, providing a linear colour scale for the colours in colour_map

symmetric

Whether to have a positive and negative colour scale (not yet implemented)

par

A list of plot parameters to pass to add_colour_bar

vertical

Whether to use a vertical (default) or horizontal colour bar.

layout

A function to generate an rgl subscene layout, generated with mfrow3d or layout3d. The function should take no arguments (a thunk).

...

additonal parameters to be passed to create_mesh

plot_corners

The coordinates in pixels for the top left and bottom right corners of the the rgl device. c(lx, ly, rx, ry)

zoom

A zoom factor to apply to each subplot. This is the inverse of what you might expect for consistency with rgl. zoom > 1 zooms out, zoom < zooms in.

add_normals

Whether or not to add normals to the surface objects, see create_mesh for details

colour_title

legend title for the colour bar if requested

close_on_output

Whether or not to close the output after taking a snapshot, defaults to TRUE

Value

The subscenes invisibly.

Details

This function is designed to do a simple 6 angle plot for statistic maps of the left and right hemispheres of subject's brain. It defaults to leaving the rgl device open so that you can take a snapshot after tweaking the angles, or changing the colour bar with add_colour_bar. Its other mode is to take a snapshot after it has finished adding the 3d objects to the scene, in this mode, whether or not to keep the window open can be configured with close_on_output.