plot-methods: Plot a NeuroSlice

In bbuchsbaum/neuroim2: Data Structures for Brain Imaging Data

Plot a NeuroSlice

Description

Plot a NeuroSlice

plot an NeuroVol as a series of 2D slices

Usage

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

## S4 method for signature 'NeuroVol'
plot(
  x,
  cmap = gray(seq(0, 1, length.out = 255)),
  zlevels = unique(round(seq(1, dim(x)[3], length.out = 6))),
  irange = range(x, na.rm = TRUE),
  thresh = c(0, 0),
  alpha = 1,
  bgvol = NULL,
  bgcmap = gray(seq(0, 1, length.out = 255))
)

Arguments

x	the object to display
cmap	a color map consisting of a vector of colors in hex format (e.g. gray(n=255))
irange	the intensity range indicating the low and high values of the color scale.
zlevels	the series of slice indices to display.
thresh	a 2-element vector indicating the lower and upper transparency thresholds.
alpha	the level of alpha transparency
bgvol	a background volume that serves as an image underlay (currently ignored).
bgcmap	a color map for backround layer consisting of a vector of colors in hex format (e.g. gray(n=255))

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.

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)

bbuchsbaum/neuroim2 documentation built on Feb. 26, 2025, 3:49 p.m.