Create Multi-Image Plot with Overlays

Creates a multi-row or multi-column plot with image slices and the potential for overlays as well.

multi_overlay(
  x,
  y = NULL,
  z = NULL,
  w = 1,
  mask = NULL,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  ybreaks = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  direction = c("horizontal", "vertical"),
  par.opts = list(oma = c(0, 0, 0, 0), mar = rep(0, 4), bg = "black"),
  text = NULL,
  text.x = 0.5,
  text.y = 1.4,
  text.cex = 2.5,
  text.col = "white",
  main = NULL,
  main.col = text.col,
  main.cex = text.cex,
  NA.x = TRUE,
  NA.y = TRUE,
  pdim = NULL,
  useRaster = TRUE,
  ...
)

multi_overlay_center(x, y = NULL, ...)

Arguments

x	List of images of class nifti or character vector of filenames
y	List of images of class nifti or character vector of filenames. Same length as x.
z	Slice to display.
w	3D volume to display if x has 4-D elements
mask	nifti image to drop empty image dimensions if wanted. Passed to dropEmptyImageDimensions
col.x	Color to display x images
col.y	Color to display y images
zlim.x	Limits for x to plot
zlim.y	Limits for y to plot
ybreaks	(numeric) breaks for y to passed to image
plane	the plane of acquisition to be displayed
xlab	Label for x-axis
ylab	Label for y-axis
axes	Should axes be displayed
direction	Should images be a row or column? Ignored if mfrow is in par.opts
par.opts	Options to pass to par
text	Text to be displayed
text.x	Location of text in x-domain
text.y	Location of text in y-domain
text.cex	Multiplier for text font
text.col	Color for text and main.
main	Title for each plot
main.col	Color for main. Will default to text.col
main.cex	Multiplier for text font. Will default to text.cex
NA.x	Should 0's in x be set to NA?
NA.y	Should 0's in y be set to NA?
pdim	Pixel dimensions if passing in arrays. Will be overridden if x is a nifti object
useRaster	if TRUE, a bitmap raster is used to plot the image instead of polygons. Passed to image
...	Additional arguments to pass to image

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,,c(3, 5)] = rpois(1000*2, lambda = 2)
nim = oro.nifti::nifti(arr)
mask = nim > 2
add_mask = nim[,,,1] > 0
imgs = img_ts_to_list(nim) 
masks = img_ts_to_list(mask) 
multi_overlay(imgs, masks)

multi_overlay(imgs, masks, 
main = "hey", direction = "vertical", plane = "coronal")

multi_overlay(imgs, masks, mask = add_mask, 
main = "hey")




if (FALSE) {

 if (requireNamespace("brainR", quietly = TRUE)) {
   visits = 1:3
   y = paste0("Visit_", visits, ".nii.gz")
   y = system.file(y, package = "brainR")
   y = lapply(y, readnii)

   y = lapply(y, function(r){
     pixdim(r) = c(0, rep(1, 3), rep(0, 4))
     dropImageDimension(r)
   })

   x = system.file("MNI152_T1_1mm_brain.nii.gz", 
                 package = "brainR")
   x = readnii(x)
   mask = x >0
   x = lapply(visits, function(tmp){
       x
   })
   alpha = function(col, alpha = 1) {
       cols = t(col2rgb(col, alpha = FALSE)/255)
       rgb(cols, alpha = alpha)
   }
   multi_overlay(x, y, 
         col.y = alpha(hotmetal(), 0.5),
         mask = mask, 
         main = paste0("\n", "Visit ", visits),
         text = LETTERS[visits],
         text.x = 0.9,
         text.y = 0.1,
         text.cex = 3)
 }
}