SpatialData label viz.

SpatialData label viz.

Usage

# S4 method for class 'SpatialData'
plotLabel(
  x,
  i = 1,
  j = 1,
  k = NULL,
  c = NULL,
  a = 0.5,
  pal = NULL,
  nan = NA,
  assay = 1,
  t = NULL,
  z = NULL
)

Arguments

x

SpatialData object.

i

character string or index; the label element to plot.

j

index or name of target coordinate system.

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.

Examples

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

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

# simple binary image
p + plotLabel(x, i)


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

# coloring by 'colData'
p + plotLabel(x, i, c="id")


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