image.im3d: Method to plot spatially calibrated image arrays

In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Method to plot spatially calibrated image arrays

Description

Method to plot spatially calibrated image arrays

Usage

## S3 method for class 'im3d'
image(
  x,
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  plotdims = NULL,
  flipdims = "y",
  filled.contour = FALSE,
  asp = 1,
  axes = FALSE,
  xlab = NULL,
  ylab = NULL,
  nlevels = 20,
  levels = pretty(zlim, nlevels + 1),
  color.palette = colorRampPalette(c("navy", "cyan", "yellow", "red")),
  col = color.palette(length(levels) - 1),
  useRaster = NULL,
  ...
)

Arguments

x	The im3d object containing the data to be plotted (NAs are allowed).
xlim, ylim	ranges for the plotted x and y values, defaulting to the BoundingBox of x.
zlim	the minimum and maximum z values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted.
plotdims	Which dimensions of 3D im3d object to plot (character vector). Defaults to c('x','y')
flipdims	Which dimensions to flip (character vector). Defaults to flipping y.
filled.contour	Whether to use a filled.contour plot instead of a regular image plot.
asp	Whether to have a a square aspect ratio (logical, default: FALSE)
axes	Whether to plot axes (default: FALSE)
xlab, ylab	each a character string giving the labels for the x and y axis. Default to the ‘call names’ of x or y, or to "" if these were unspecified.
nlevels	The number of colour levels in z
levels	The levels at which to break z values
color.palette	The colour palette from which col will be selected.
col	a list of colors such as that generated by rainbow, heat.colors, topo.colors, terrain.colors or similar functions.
useRaster	Whether to use rasterImage to plot images as a bitmap (much faster for large images). default useRaster=NULL checks dev.capabilities to see if raster images are supported.
...	graphical parameters for plot or image may also be passed as arguments to this function.

Value

A list with elements:

zlim

The z (intensity limits)

nlevels.actual

The actual number of plotted levels

nlevels.orig

The requested number of plotted levels

levels

The chosen levels

colors

A character vector of colours

Examples

## Not run: 
LHMask=read.im3d(system.file('tests/testthat/testdata/nrrd/LHMask.nrrd',package='nat'))
image(imslice(LHMask,10), asp=TRUE)
# useRaster is appreciably quicker in most cases
image(imslice(LHMask,10), asp=TRUE, useRaster=TRUE)

## End(Not run)

nat documentation built on May 29, 2024, 10:36 a.m.