orthographic-methods: Methods for Function 'orthographic' in Package 'dcemriS4'
In oro.nifti: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output

orthographic-methods

R Documentation

Methods for Function ‘orthographic’ in Package ‘dcemriS4’

Description

Produce orthographic display for nifti, anlz and afni objects.

Usage

orthographic.nifti(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

orthographic(x, ...)

## S4 method for signature 'nifti'
orthographic(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

## S4 method for signature 'anlz'
orthographic(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

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

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

Arguments

`x`	is an object of class `nifti` or similar.
`y`	is an object of class `nifti` or similar for the overlay.
`xyz`	is the coordinate for the center of the crosshairs.
`w`	is the time point to be displayed (4D arrays only).
`col`	is grayscale (by default).
`col.y`	is hotmetal (by default).
`zlim`	is the minimum and maximum ‘z’ values passed into `image`.
`zlim.y`	is the minimum and maximum ‘z’ values passed into `image` for the overlay.
`crosshairs`	is a logical value for the presence of crosshairs in all three orthogonal planes (default = TRUE).
`col.crosshairs`	is the color of the crosshairs (default = red).
`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.
`text`	allows the user to specify text to appear in the fourth (unused) pane.
`text.color`	is the color of the user-specified text (default = “white”.
`text.cex`	is the size of the user-specified text (default = 2).
`...`	other arguments to the `image` function may be provided here.

Methods

x = "afni": Produce orthographic display for x.
x = "anlz": Produce orthographic display for x.
x = "array": Produce orthographic display for x.
x = "nifti": Produce orthographic display for x.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

Examples

fname = system.file(
file.path("nifti", "mniRL.nii.gz"),
package = "oro.nifti")
eve = readNIfTI(fname)
orthographic(eve)

image(eve, z = 45)
image(eve, z = 45, plot.type = "single")
image(eve, z = c(45, 50), plot.type = "single")

oro.nifti documentation built on Aug. 10, 2022, 5:09 p.m.