ortho2: Orthographic Display, added options

In neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Orthographic Display, added options

Description

Copy of oro.nifti's orthographic function with some tweaks such as adding L/R designations for left and right

Usage

ortho2(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = oro.nifti::hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  NA.x = FALSE,
  NA.y = TRUE,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = c(0, 0, 0, ifelse(ycolorbar, 5, 0)),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  text.x = 32,
  text.y = 32,
  add.orient = FALSE,
  mfrow = c(2, 2),
  ybreaks = NULL,
  breaks = NULL,
  addlegend = FALSE,
  leg.x = 32,
  leg.y = 32,
  legend,
  leg.col,
  leg.title = NULL,
  leg.cex,
  window = NULL,
  ycolorbar = FALSE,
  clabels = TRUE,
  add = TRUE,
  pdim = NULL,
  useRaster = is.null(y),
  mask = NULL,
  ...
)

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.
NA.x	Set any values of 0 in x to NA
NA.y	Set any values of 0 in y to NA
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).
text.x	x coordinate for text
text.y	y coordinate for text
add.orient	(logical) Add left/right, A/P, etc. orientation
mfrow	(numeric) layout of the 3 slices
ybreaks	(numeric) breaks for y to passed to image
breaks	(numeric) breaks for x to passed to image
addlegend	(logical) add legend?
leg.x	(numeric) x coordinate for legend
leg.y	(numeric) y coordinate for legend
legend	(character) legend text
leg.col	(character) Colors for legend
leg.title	(character) title for legend
leg.cex	(numeric) cex for legend
window	(vector) Length-2 vector to limit image to certain range
ycolorbar	(logical) Should a colorbar for y be plotted
clabels	Label for colorbar (see colorbar)
add	Should the y-plot be added or its own plot? Used in double_ortho
pdim	Pixel dimensions if passing in arrays. Will be overridden if x is a nifti object
useRaster	logical; if TRUE a bitmap raster is used to plot the image instead of polygons. Passed to image.
mask	If a mask is passed, drop_empty_dim is applied to both x and y
...	other arguments to the image function may be provided here.

See Also

orthographic

Examples

set.seed(10)
x = oro.nifti::nifti(array(rnorm(1000), dim = rep(10, 3)))
ortho2(x)
y = x > 2
mask = x > 2.5
ortho2(x, y)
ortho2(x, y, mask = mask, add.orient = TRUE)
ortho2(x, y, mask = mask, add.orient = TRUE, add = FALSE)
nim = RNifti::asNifti(x, internal = FALSE)
ortho2(nim, y, mask = mask)
neurobase::ortho2(nim, x, mask = mask, 
ybreaks = seq(min(x), max(x), length.out = 65), ycolorbar = TRUE)

ortho2(nim, y, mask = mask, add = FALSE)
arr_x = as.array(x)
arr_y = as.array(y)
ortho2( arr_x)
ortho2( arr_x, arr_y, useRaster = FALSE)

set.seed(10)
x = oro.nifti::nifti(array(rnorm(10000), dim = rep(10, 4)))
y = x > 2
mask = x > 2.5
ortho2(x, y)

set.seed(10)
x = oro.nifti::nifti(array(rnorm(100), dim = rep(10, 2)))
y = x > 2
mask = x > 2.5
ortho2(x, y)

neurobase documentation built on May 29, 2024, 2:17 a.m.