plot.antsImage: Plotting an image slice or multi-slice with optional color...

In muschellij2/atropos: Core Software Infrastructure for 'ANTsR'

Description

This is a plotting utility for antsImage types with a background and color overlay option. Useful for displaying statistical results overlaid on a background image.

Usage

## S3 method for class 'antsImage'
plot(x, y, color.img = "white",
  color.overlay = c("jet", "red", "blue", "green", "yellow", "viridis",
  "magma", "plasma", "inferno"), axis = 2, slices,
  colorbar = missing(y), title.colorbar, title.img, title.line = NA,
  color.colorbar, window.img, window.overlay, quality = 2,
  outname = NA, alpha = 1, direction = 1, begin = 0, end = 1,
  newwindow = FALSE, nslices = 10, domainImageMap = NA,
  ncolumns = 4, useAbsoluteScale = FALSE, doCropping = TRUE, text,
  ...)

Arguments

x	the reference image on which to overlay.
y	image or list of images to use as overlays.
color.img	color for main image.
color.overlay	the color for the overlay , e.g c('blue','red') length of this list should match the image list.
axis	the axis to slice (1 , 2 or 3)
slices	vector of slices to plot (e.g., c(10, 15, 20))
colorbar	make colorbar?
title.colorbar	title for colorbar
title.img	title for main image (not displayed when file is saved with outname)
title.line	title vertical displacement (irrelevant when a file is saved with outname)
color.colorbar	color scale to use for colorbar
window.img	lower and upper thresholds for display of main image
window.overlay	lower and upper thresholds for display of overlay. if you set window.overlay = c( 0, 100 ) and useAbsoluteScale=T then the image overlay will map into that range. otherswise, the min and max of the image will be used.
quality	integer quality magnification factor 1 => large (e.g. 10)
outname	name of output file if you want to write result to file, e.g. plot.jpg.
alpha	opacity
direction	Sets the order of colors in the scale. If 1, the default, colors are ordered from darkest to lightest. If -1, the order of colors is reversed.
begin	The (corrected) hue in [0,1] at which the viridis colormap begins.
end	The (corrected) hue in [0,1] at which the viridis colormap ends
newwindow	boolean controlling if we open a new device for this plot
nslices	number of slices to view
domainImageMap	this input antsImage or list contains a reference image (domainImage) and optional reference mapping named domainMap. these will be used to map the input image(s) to this antsImage space before plotting. this is useful for non-standard image orientations.
ncolumns	number of columns in plot
useAbsoluteScale	boolean determines whether dynamic range is maximized when visualizing overlays
doCropping	apply cropping, defaults to TRUE
text	vector containing x, y, label, cex and color values passed to text command, e.g. txt=list(x=0,y=0,label='my text',cex=2,col='red')
...	other parameters

Value

output is plot to standard R window

Author(s)

Avants BB

Examples

img <- makeImage(c(4,4), rnorm(4*4))
mask <- makeImage(c(4,4),
   as.matrix(c(0,0,0,0,
            0,1,1,0,
            0,1,1,0,
            0,0,0,0), nrow=4))
plot(img, list(mask))
txt=list(x=2.5,y=1.5,label='my text',cex=4,col='red')
plot(img, list(mask), text=txt)
testthat::expect_error(plot(multi_component_image))

## Not run: 

  img = antsImageRead( getANTsRData( 'r16' ) )
  betaVals = rnorm( prod( dim( img ) ), 0, 20 )
  betaImg = makeImage( dim( img ), betaVals )  %>% smoothImage( 3.5 )
  betaImg[ abs( betaImg ) < 1.5 ] = 0
  plot( img, betaImg, window.img=range(img) ,window.overlay=range(betaImg) )

  mnit<-getANTsRData('mni')
  mnit<-antsImageRead(mnit)
  mniafn<-getANTsRData('mnia')
  mnia<-antsImageRead(mniafn)
  mnia<-thresholdImage(mnia,22,25)
  mnia<-smoothImage(mnia,1.5)
  mnia2<-antsImageRead(mniafn)
  mnia2<-thresholdImage(mnia2,1,4)
  mnia2<-smoothImage(mnia2,1.5)
  ofn<-paste(tempfile(),'.png',sep='')
  # write directly to a file
  plot( mnit, list(mnia,mnia2), slices=seq(50, 140, by=5),
    window.overlay = c(0.25,1), axis=2,
    color.overlay=c('red','blue'), outname = ofn )

## End(Not run)

muschellij2/atropos documentation built on May 4, 2019, 3:17 p.m.