display: Image Display

In EBImage: Image processing and analysis toolbox for R

Description

Display images in an interactive JavaScript viewer or using R's built-in graphics capabilities.

Usage

display(x, method, ...)

## S3 method for class 'Image'
plot(x, ...)

Arguments

x	an Image object or an array.
method	the way of displaying images. Defaults to "browser" when R is used interactively, and to "raster" otherwise. The default behavior can be overridden by setting options("EBImage.display"). See Details.
...	arguments to be passed to the specialized display functions; for details see the sections on individual display methods.

Details

The default method used for displaying images depends on whether called from and interactive R session. If interactive() is TRUE images are displayed with the "browser" method, otherwise the "raster" method is used. This dynamic behavior can be overridden by setting options("EBImage.display") to either "browser" or "raster".

plot.Image S3 method is a wrapper for display(..., method="raster")

"browser" method

The "browser" method runs an interactive JavaScript image viewer. A list of available features along with corresponding mouse and keyboard actions is shown by pressing 'h'. This method takes the following additional arguments.

embed

logical(1), include images in the document as data URIs. Defaults to TRUE in non-interactive context (e.g. static R Markdown documents), otherwise to FALSE.

tempDir

character(1), file path for storing any temporary image files. Defaults to tempfile("")

...

arguments passed to createWidget, such as fixed width and height (in CSS units), elementId, or preRenderHook.

"raster" method

The "raster" method displays images as R raster graphics. The user coordinates of the plotting region are set to the image pixel coordinates with the origin (0, 0) in the upper left corner.

By default only the first frame of an image stack is shown; a different frame can also be specified. When all=TRUE the whole image stack is rendered and the frames are automatically positioned next to each other in a grid. The grid layout can be modified through nx and spacing and margin.

This method provides to following additional arguments to display.

interpolate

a logical vector (or scalar) indicating whether to apply linear interpolation to the image when drawing.

frame

a numeric indicating the frame number to display; only effective when all = FALSE.

all

logical, defaulting to FALSE. If set to TRUE, all frames of a stacked image are displayed arranged in a grid, otherwise (default) just a single frame specified in frame is displayed. The grid layout can be controlled by nx, spacing and margin.

drawGrid

a logical indicating whether to draw grid lines between individual frames. Defaults to TRUE unless spacing is non-zero. Line color, type and width can be specified through graphical parameters col, lty and lwd, respectively; see par for details.

nx

integer. Specifies the number images in a row. Negative numbers are interpreted as the number of images in a column, e.g. use -1 to display a single row containing all the frames.

spacing

numeric. Specifies the separation between frames as a fraction of frame dimensions (positive numbers <1) or in pixels (numbers >=1). It can be either a single number or a vector of length 2, in which case its elements correspond to the horizontal and vertical spacing, respectively.

margin

numeric. Specifies the outer margins around the image, or a grid of images. Similarly as for spacing, different horizontal and vertical margins can be defined by providing a vector.

...

graphical parameters passed to par

Author(s)

Andrzej Oles, [e-mail], 2012-2017

See Also

display-shiny

Examples

## Display a single image
x = readImage(system.file("images", "sample-color.png", package="EBImage"))[257:768,,]
display(x)

## Display a thresholded sequence ...
y = readImage(system.file("images", "sample.png", package="EBImage"))[366:749, 58:441]
z = lapply(seq(from=0.5, to=5, length=6),
  function(s) gblur(y, s, boundary="replicate")
)
z = combine(z)

## ... using the interactive viewer ...
display(z)

## ... or using R's build-in raster device
display(z, method = "raster", all = TRUE)

## Display the last frame 
display(z, method = "raster", frame = numberOfFrames(z, type = "render"))

## Customize grid appearance
display(z, method = "raster", all = TRUE,
        nx = 2, spacing = 0.05, margin = 20, bg = "black")

Example output

Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.

EBImage documentation built on Nov. 8, 2020, 5:41 p.m.