Add image layer to SpatialData plot

Add image layer to SpatialData plot

Usage

plotImage(
  i = 1,
  j = NULL,
  k = NULL,
  ch = NULL,
  c = NULL,
  cl = NULL,
  t = NULL,
  z = NULL,
  x = NULL
)

Arguments

i

Index or name of image to plot.

j

Index or name of coordinate transformation to use. If NULL, the coordinate transformation will be inherited from plotSpatialData().

k

Index of the scale to render; by default (NULL), will auto-select scale in order to minimize memory-usage and blurring for a target size of 800 x 800px; use Inf to plot the lowest resolution available.

ch

Image channel(s) to be used for plotting (defaults to the first channel(s) available); use channels() to see which channels are available for a given SpatialDataImage

c

Character vector; colors to use for each channel.

cl

List of length-2 numeric vectors (non-negative, increasing); specifies channel-wise contrast limits - defaults to [0, 1] for all (ignored when image(x, i) is an RGB image; for convenience, any NULL = [0, 1], and n = [0, n]).

t, z

Integer scalar to indicate a specific time- or z-slice; if left unspecified (default NULL), will perform a max-projection.

x

SpatialData object. If NULL, the object will be inherited from plotSpatialData().

Value

An object of type sd_image, which can be added to an existing ggplot.

Examples

x <- file.path("extdata", "blobs.zarr")
x <- system.file(x, package="spatialdataR")
x <- readSpatialData(x, tables=FALSE)

ms <- lapply(seq(3), \(.) 
  plotSpatialData(x) +
  plotImage(2, k=.))
patchwork::wrap_plots(ms)


# custom colors
cmy <- c("cyan", "magenta", "yellow")
plotSpatialData(x) + plotImage(c=cmy)


# contrast limits
cl <- rep(list(c(0, 1/3)), 3)
plotSpatialData(x, ct="global") + 
  plotImage(k=1, c=cmy, cl=cl) + 
  plotShape(i="blobs_circles", fill="pink") + 
  plotPoint(i="blobs_points", colour="instance_id")
#> Coordinate system already present.
#> ℹ Adding new coordinate system, which will replace the existing one.
#> Coordinate system already present.
#> ℹ Adding new coordinate system, which will replace the existing one.