Plot spatial transcriptomic annotations per spot

Usage

plotSpatial(
  spe,
  what = c("annotation", "expression", "reduceddim"),
  ...,
  assay = SummarizedExperiment::assayNames(spe),
  dimred = SingleCellExperiment::reducedDimNames(spe),
  img = FALSE,
  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").
...: additional aesthetic mappings or fixed parameters (e.g., shape = ".").
assay: a character or numeric, specifying the assay to plot (default is the first assay).
dimred: a character or numeric, specifying the reduced dimension to plot (default is the first reduced dimension).
img: a logical, indicating whether the tissue image (if present) should be plot (default = FALSE).
crop: a logical, indicating whether the image should be cropped to the spatial coordinates (default = FALSE).
imgAlpha: a numeric, specifying the alpha value for the image (default = 1).
rl: a numeric, specifying the relative size of the text (default = 1).
circles: a logical, indicating whether the spots should be plotted as circles (default = FALSE). This can be slower for large datasets.

Value

a ggplot2 object

Examples

library(SpatialExperiment)
library(ggplot2)

# load data
data(HumanDLPFC)

# plot spatial region annotations
p1 <- plotSpatial(HumanDLPFC, colour = AnnotatedCluster)
p1


# change colour scale
p1 + scale_colour_brewer(palette = "Paired")
#> Warning: Removed 127 rows containing missing values or values outside the scale range
#> (`geom_point()`).


# plot spatial expression
plotSpatial(HumanDLPFC, what = "expression", colour = ENSG00000075624) +
 scale_colour_viridis_c(option = "F")


# plot logcounts
logcounts(HumanDLPFC) <- log2(counts(HumanDLPFC) + 1)
plotSpatial(HumanDLPFC, what = "expression", colour = ENSG00000075624, assay = "logcounts") +
 scale_colour_viridis_c(option = "F")


# change point shape
plotSpatial(HumanDLPFC, what = "expression", colour = ENSG00000075624, assay = "logcounts", shape = 18) +
 scale_colour_viridis_c(option = "F")