SpatialData image viz.

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Usage

# S4 method for class 'SpatialData'
plotImage(x, i = 1, j = 1, k = NULL, ch = NULL, c = NULL, cl = NULL)

plotSpatialData()

Arguments

x

SpatialData object.

i

element to use from a given layer.

j

name of target coordinate system.

k

index of the scale of an image; 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]).

Value

ggplot

Examples

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

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


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


# contrast limits
cl <- rep(list(c(0, 1/3)), 3)
plotSpatialData() + plotImage(x, k=1, c=cmy, cl=cl)