plot-methods: Plot a NeuroSlice

In neuroim2: Data Structures for Brain Imaging Data

Plot a NeuroSlice

Description

Display axial slices of a NeuroVol as a faceted montage.

Usage

## S4 method for signature 'NeuroSlice,ANY'
plot(
  x,
  cmap = gray(seq(0, 1, length.out = 255)),
  irange = range(x, na.rm = TRUE),
  legend = TRUE
)

## S4 method for signature 'NeuroVol,missing'
plot(
  x,
  y,
  cmap = "grays",
  zlevels = unique(round(seq(1, dim(x)[3], length.out = 9))),
  irange = range(x, na.rm = TRUE),
  thresh = c(0, 0),
  alpha = 1,
  legend = TRUE
)

## S4 method for signature 'NeuroVol,NeuroVol'
plot(
  x,
  y,
  cmap = "grays",
  zlevels = unique(round(seq(1, dim(x)[3], length.out = 9))),
  ov_cmap = "inferno",
  ov_alpha = 0.5,
  ov_thresh = 0
)

Arguments

x	the background volume to display.
cmap	palette name or hex-color vector for the background (default "grays"). See resolve_cmap.
irange	numeric length-2 intensity range for the color scale.
legend	logical; show the colour bar?
y	optional overlay volume (same dimensions as x). When supplied, the plot is rendered as a background + overlay composite.
zlevels	integer slice indices to display. Default: 9 evenly-spaced slices (3 \times 3 grid).
thresh	a 2-element vector indicating the lower and upper transparency thresholds.
alpha	opacity for the background layer (0–1).
ov_cmap	overlay palette name (default "inferno").
ov_alpha	overlay opacity (default 0.5).
ov_thresh	overlay threshold; values with |v| < ov_thresh become transparent (default 0).

Details

The plot method uses ggplot2 to create a raster visualization of the slice data. The intensity values are mapped to colors using the specified colormap and range.

when 'x' is a NeuroSlice object, the plot method returns a ggplot2 object containing the raster visualization of the slice data. The plot can be further customized using standard ggplot2 functions.

When a second volume y is supplied it is treated as an overlay (e.g.\ a statistical map) composited on top of x with adjustable transparency. This delegates to plot_overlay.

Value

a ggplot2 object

Examples

# Create example slice
slice_space <- NeuroSpace(c(100, 100))
slice_data <- matrix(rnorm(100*100), 100, 100)
slice <- NeuroSlice(slice_data, slice_space)

# Basic plot
plot(slice)



dat <- matrix(rnorm(100*100), 100, 100)
slice <- NeuroSlice(dat, NeuroSpace(c(100,100)))

plot(slice)

neuroim2 documentation built on April 16, 2026, 5:07 p.m.