R: Methods for Function 'slice'

slice-methods {oro.nifti}

R Documentation

Methods for Function ‘slice’

Description

Produce “lightbox” layout of slices for nifti, anlz and afni objects.

Usage

slice(x, ...)

## S4 method for signature 'nifti'
slice(
  x,
  z = 1,
  w = 1,
  col = gray(0:64/64),
  plane = c("axial", "coronal", "sagittal"),
  zlim = NULL,
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  useRaster = TRUE,
  ...
)

## S4 method for signature 'anlz'
slice(
  x,
  z = 1,
  w = 1,
  col = gray(0:64/64),
  plane = c("axial", "coronal", "sagittal"),
  zlim = NULL,
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  useRaster = TRUE,
  ...
)

## S4 method for signature 'array'
slice(x, ...)

## S4 method for signature 'afni'
slice(x, ...)

Arguments

`x`	is an object of class `nifti` or similar.
`...`	other arguments to the `image` function may be provided here.
`z`	is the slice to be displayed (ignored when `plot.type = "multiple"`).
`w`	is the time point to be displayed (4D arrays only).
`col`	is grayscale (by default).
`plane`	is the plane of acquisition to be displayed (choices are ‘axial’, ‘coronal’, ‘sagittal’).
`zlim`	is set to `NULL` by default and utilizes the internal image range.
`xlab`	is set to “” since all margins are set to zero.
`ylab`	is set to “” since all margins are set to zero.
`axes`	is set to `FALSE` since all margins are set to zero.
`oma`	is the size of the outer margins in the `par` function.
`mar`	is the number of lines of margin in the `par` function.
`bg`	is the background color in the `par` function.
`useRaster`	if `TRUE`, a bitmap raster is used to plot the image instead of polygons. Passed to `image`

Details

Uses the S3 generic function slice, with medical-image friendly settings, to display nifti, anlz and afni class objects in a “lightbox” layout.

Methods

x = "ANY": Generic function: see image.
x = "nifti": Produce images for x.
x = "anlz": Produce images for x.
x = "afni": Produce images for x.

Author(s)

Brandon Whitcher bwhitcher@gmail.com