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

Description Usage Arguments Value Author(s) Examples

View source: R/plot.antsImage.R

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

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## 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

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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 Oct. 11, 2018, 12:24 a.m.