plot-methods: Visualize 2D Neuroimaging Slice

In bbuchsbaum/neuroim2: Data Structures and IO for Neuroimaging Data with an Emphasis on Functional Magnetic Resonance Imaging (FMRI)

Visualize 2D Neuroimaging Slice

Description

Creates a 2D visualization of a NeuroSlice object using ggplot2.

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))
...	Additional arguments passed to plotting methods

Details

Plot a NeuroSlice Object

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.

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)

## Not run: 
# Basic plot
plot(slice)

# Custom colormap
library(viridis)
plot(slice, cmap = viridis(255))

# Custom intensity range
plot(slice, irange = c(-2, 2))

## End(Not run)


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

bbuchsbaum/neuroim2 documentation built on Jan. 2, 2025, 3:38 p.m.