overlay-methods: Methods for Function overlay

In muschellij2/oro.nifti: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output

Methods for Function overlay

Description

Methods for function overlay

Usage

overlay.nifti(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

overlay(x, y, ...)

## S4 method for signature 'nifti,missing'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'nifti,nifti'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'anlz,anlz'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'anlz,nifti'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'nifti,anlz'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

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

## S4 method for signature 'array,nifti'
overlay(x, y, ...)

## S4 method for signature 'nifti,array'
overlay(x, y, ...)

## S4 method for signature 'array,anlz'
overlay(x, y, ...)

## S4 method for signature 'anlz,array'
overlay(x, y, ...)

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

## S4 method for signature 'afni,array'
overlay(x, y, ...)

Arguments

x, y	is an object of class nifti or similar.
z	is the slice to be displayed (ignored when plot.type = "multiple").
w	is the time point to be displayed (4D arrays only).
col.x	is grayscale (by default).
col.y	is hotmetal (by default).
zlim.x, zlim.y	are set to NULL (by default) and taken from the header information.
plane	is the plane of acquisition to be displayed (choices are ‘axial’, ‘coronal’, ‘sagittal’).
plot.type	allows the choice between all slices being displayed, in a matrix (left-to-right, top-to-bottom), or a single slice.
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.
NA.x	Set any values of 0 in x to NA
NA.y	Set any values of 0 in y to NA
...	other arguments to the image function may be provided here.

Details

The image command is used multiple times to simultaneously visualize one of the three orthogonal planes in two multidimensional arrays, one on top of the other, for medical imaging data.

Methods

x = "nifti", y = "nifti"

Produce overlay of y on x.

x = "anlz", y = "anlz"

Produce overlay of y on x.

x = "afni", y = "afni"

Produce overlay of y on x.

Author(s)

Brandon Whitcher [e-mail]

See Also

image-methods, overlay-methods

muschellij2/oro.nifti documentation built on Nov. 28, 2023, 5:36 a.m.