Plot cells based on cell position on tissue.

Plot cells based on cell position on tissue.

Usage

plotTissue(
  spe,
  targetcell = FALSE,
  k_near = 100,
  targetsize = 3,
  targetshape = 1,
  targetcolor = "red",
  scaleFactor = 1,
  reverseY = TRUE,
  ...
)

Arguments

spe

SpatialExperiment object.

targetcell

Optional. Can input ONE specific cell id to zoom-in on the region of a specific cell.

k_near

Optional. If targetcell is specified, the k_near cells around the targetcell will be plotted.

targetsize

Dot size of the targetcell.

targetshape

Shape of the targetcell.

targetcolor

Colour of the targetcell.

scaleFactor

Scale factor to align with the image.

reverseY

Reverse y coordinates.

...

aesthetic mappings to pass to ggplot2::aes_string().

Value

A ggplot object.

Examples

data("spe_test")

plotTissue(spe, color = celltypes)