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 = c("red", "green"),
  nan = NA,
  assay = 1
)

Arguments

x

SpatialData object.

i

character string or index; the label element to plot.

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.

c

the default, NULL, gives a binary image of whether or not a given pixel is non-zero; alternatively, a character string specifying a colData column or row name in a table annotating i.

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).

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 valTable).

Examples

x <- system.file("extdata", "blobs.zarr", package="SpatialData")
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'
n <- length(unique(t$id))

# pal <- hcl.colors(n, "Spectral")
pal_d <- hcl.colors(10, "Spectral")
p + plotLabel(x, i, c="id", pal=pal_d)


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