neurobase (version 1.32.4)

ortho2: 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)