ortho2 | R Documentation |
Copy of oro.nifti
's orthographic
function
with some tweaks such as adding L/R designations for left and right
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,
...
)
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 |
NA.y |
Set any values of 0 in |
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
|
breaks |
(numeric) breaks for x to passed to
|
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) |
window |
(vector) Length-2 vector to limit image to certain range |
ycolorbar |
(logical) Should a colorbar for |
clabels |
Label for colorbar (see |
add |
Should the y-plot be added or its own plot? Used
in |
pdim |
Pixel dimensions if passing in arrays. Will be overridden if
|
useRaster |
logical; if TRUE a bitmap raster is used to
plot the image instead of polygons. Passed to
|
mask |
If a mask is passed, |
... |
other arguments to the image function may be provided here. |
orthographic
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)
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