Add label layer to SpatialData plot

Usage

plotLabel(
  i = 1,
  j = NULL,
  k = NULL,
  c = NULL,
  a = 0.5,
  pal = NULL,
  nan = NA,
  assay = 1,
  t = NULL,
  z = NULL,
  x = NULL
)

Arguments

i: Index or name of label 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.
c: determines label colors; the default (NULL), gives a binary image of whether or not a pixel is non-zero; alternatively, a character string specifying a colData column or row name in an annotation table.
a: scalar numeric in [0, 1]; alpha value passed to geom_tile.
pal: character vector; color for discrete/continuous values (interpolated automatically when insufficient values are provided). When left unspecified, color will be sampled at random.
nan: character string; color for missing values (hidden by default).
assay: character string; in case of c denoting a row name, specifies which assay data to use (see getTable).
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_label, which can be added to an existing ggplot.

Examples

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

i <- "blobs_labels"
p <- plotSpatialData(x)

# simple binary image
p + plotLabel(i)


# mock up some extra data
t <- getTable(x, i)
t$id <- sample(letters, ncol(t))
table(x) <- t

# coloring by 'colData'
t <- getTable(x, i)
t$id <- sample(letters, ncol(t))
table(x) <- t
plotSpatialData(x) + plotLabel(i=i, c="id")


# coloring by 'assay' data
plotSpatialData(x) + plotLabel(i=i, 
  c="channel_1_sum", 
  pal=c("lavender", "blue"))