plot.antsImage.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot.antsImage.R
\name{plot.antsImage}
\alias{plot.antsImage}
\title{Plotting an image slice or multi-slice with optional color overlay.}
\usage{
\method{plot}{antsImage}(
  x,
  y = NULL,
  color.img = "white",
  color.overlay = c("jet", "red", "blue", "green", "yellow", "viridis", "magma",
    "plasma", "inferno"),
  axis = 2,
  slices,
  colorbar = FALSE,
  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 = NULL,
  ncolumns = 4,
  useAbsoluteScale = FALSE,
  doCropping = TRUE,
  text,
  ...
)
}
\arguments{
\item{x}{the reference image on which to overlay.}

\item{y}{image or list of images to use as overlays.}

\item{color.img}{color for main image.}

\item{color.overlay}{the color for the overlay , e.g c('blue','red') length
of this list should match the image list.}

\item{axis}{the axis to slice (1 , 2 or 3)}

\item{slices}{vector of slices to plot (e.g., c(10, 15, 20))}

\item{colorbar}{make colorbar?}

\item{title.colorbar}{title for colorbar}

\item{title.img}{title for main image (not displayed when file is saved with outname)}

\item{title.line}{title vertical displacement (irrelevant when a file is saved with outname)}

\item{color.colorbar}{color scale to use for colorbar}

\item{window.img}{lower and upper thresholds for display of main image}

\item{window.overlay}{lower and upper thresholds for display of overlay.
if you set \code{window.overlay = c( 0, 100 )} and \code{useAbsoluteScale=T}
then the image overlay will map into that range.  otherswise, the min and
max of the image will be used.}

\item{quality}{integer quality magnification factor 1 => large (e.g.
10)}

\item{outname}{name of output file if you want to write result to file, e.g.
\code{plot.jpg}.}

\item{alpha}{opacity}

\item{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.}

\item{begin}{The (corrected) hue in [0,1] at which the viridis colormap
begins.}

\item{end}{The (corrected) hue in [0,1] at which the viridis colormap
ends}

\item{newwindow}{boolean controlling if we open a new device for this plot}

\item{nslices}{number of slices to view}

\item{domainImageMap}{this input antsImage or list contains a reference image
(\code{domainImage}) and optional reference mapping named \code{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.}

\item{ncolumns}{number of columns in plot}

\item{useAbsoluteScale}{boolean determines whether dynamic range is maximized
when visualizing overlays}

\item{doCropping}{apply cropping, defaults to \code{TRUE}}

\item{text}{vector containing x, y, label, cex and color values passed to
text command, e.g. \code{txt=list(x=0,y=0,label='my text',cex=2,col='red')}}

\item{...}{other parameters}
}
\value{
output is plot to standard R window
}
\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.
}
\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))

\dontrun{

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
)
}

}
\author{
Avants BB
}