plotVisiumImg: Plot Visium sample on top of H&E

In iaaka/visutils: QC, analyse and visualize visium

Plot Visium sample on top of H&E

Description

Normally this function shouldn't be called directly. Use plotVisium instead

Usage

plotVisiumImg(
  xy,
  img,
  scale.factor,
  spot.radius,
  cex = 1,
  col = "red",
  border = NA,
  spot.dist = NULL,
  img.alpha = 1,
  xlim = NULL,
  ylim = NULL,
  symmetric.lims = TRUE,
  xlab = "",
  ylab = "",
  pie.fracs = NULL,
  pie.cols = NULL,
  pie.min.frac = 0.05,
  he.img.width = NULL,
  he.grayscale = FALSE,
  ...
)

Arguments

xy	seu@images[.]@coordinates
img	image (3D array)
scale.factor	see @images[.]@scale.factors$lowres
spot.radius	see @images[.]@spot.radius
cex	spot size
col	spot color
border	color of spot border
spot.dist	distance between spots (computed from xy by default)
img.alpha	alpha level for H&E image
xlim, ylim, xlab, ylab	parameters of plot function
symmetric.lims	logical, specifies whether image crop should be square
pie.fracs	if specified plots pies instead of simple cycles. Matrix with number of rows equal to the number of spots, and number of columns equal to pie pieces.
pie.cols	colors to be used for pie pieces (ncol(pie.fracs) should be equal to length(pie.cols))
pie.min.frac	all pieces with relative size less than pie.min.frac will be discared
he.img.width	integer, defines width (in pixels) the H&E figure should be resized to. No resizing if NULL (default)
he.grayscale	logical, specifies whether H&E image should be converted to grayscale
...	other parameters to be passed to plot function

Value

data.frame with user spot coordinates

iaaka/visutils documentation built on Jan. 17, 2025, 11:29 p.m.