makePseudoVisium

Generates a visium-like array of spots across a provided spatial extent.

Usage

makePseudoVisium(
  extent = NULL,
  micron_scale = 1,
  micron_size = deprecated(),
  name = "pseudo_visium"
)

Arguments

extent

SpatExtent or anything else a SpatExtent can be extracted or created from

micron_scale

scalefactor needed to convert the target coordinate space to microns. For supported datasets, this can be found from instructions(gobject, "micron_scale"). See details.

micron_size

deprecated. Use micron_scale

name

character. (default is 'pseudo_visium') Name of giottoPolygon object to create

Value

A giottoPolygon for the pseudo-visium spots.

Details

This function generates a pseudo-Visium array of spots across the spatial extent provided. The micron_scale param is used to determine the scaling of the array relative to the target coordinate system.

micron_scale

If a is microns and b is dataset coordinate units, micron_scale is calculated as a / b.

Examples

e <- ext(0, 2000, 0, 2000)
x <- makePseudoVisium(extent = e, micron_scale = 1)
#> 449 polygons generated
plot(x)