plotSpots: Plot spatial transcriptomic annotations per spot

In bhuvad/restools: Research tools for data science projects

Plot spatial transcriptomic annotations per spot

Description

Plot spatial transcriptomic annotations per spot

Usage

plotSpots(
  spe,
  what = c("annotation", "expression", "reduceddim"),
  ...,
  assay = SummarizedExperiment::assayNames(spe),
  dimred = SingleCellExperiment::reducedDimNames(spe),
  img = TRUE,
  crop = FALSE,
  imgAlpha = 1,
  rl = 1,
  circles = FALSE
)

Arguments

spe	a SpatialExperiment object.
what	a character specifying what aspect should be plot, "annotation", "expression" or reduced dimension ("reduceddim").
...	aesthetic mappings to pass to 'ggplot2::aes_string()'.
assay	a numeric or character, specifying the assay to use (for SummarizedExperiment).
dimred	a string or integer scalar indicating the reduced dimension result in 'reducedDims(object)' to plot.
img	a logical indicating whether the tissue image (if present) should
rl	a numeric, specifying the relative scale factor to apply to text on the plot.

Value

a ggplot2 object

bhuvad/restools documentation built on June 16, 2024, 12:44 a.m.