Spatial spot plot

Usage

SpatialSpotPlot(
  srt,
  group.by = NULL,
  features = NULL,
  assay = NULL,
  layer = "data",
  values = NULL,
  plot_type = c("point", "pie"),
  plot.data = NULL,
  spot.by = NULL,
  color.by = NULL,
  geom = c("point", "jitter"),
  image = NULL,
  overlay_image = TRUE,
  image.alpha = 1,
  crop = TRUE,
  coord.cols = c("col", "row"),
  flip.y = TRUE,
  show_axes = FALSE,
  split.by = NULL,
  cells = NULL,
  show_na = FALSE,
  pt.size = NULL,
  pie.radius = NULL,
  pie.radius.scale = 0.45,
  pt.alpha = 0.9,
  stroke = 0.1,
  jitter_width = 0.25,
  jitter_height = 0.25,
  palette = "Spectral",
  palcolor = NULL,
  bg_color = "grey20",
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = NULL,
  theme_use = "theme_spatial",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  verbose = TRUE,
  image.scale = c("lowres", "hires")
)

Arguments

srt: A Seurat object.
group.by: Metadata columns to color spots by.
features: Features to color spots by (from assay/layer).
assay: Assay to use. NULL uses the default assay.
layer: Assay layer to use.
values: Spot-level values (named vector, matrix, or data.frame).
plot_type: "point" or "pie". Pie uses numeric group.by columns, values, or "<prefix>_prop_*"/"<prefix>_frac_*" when group.by is "<prefix>_dominant_type".
plot.data, spot.by, color.by: Long-format data for repeated spatial points (e.g. cell-to-spot assignments).
geom: "point" or "jitter" for plot.data.
image: Spatial image name. Required when multiple images are present; a single image is selected automatically when NULL.
overlay_image, image.alpha: Draw the spatial image beneath spots.
crop: Crop the panel to plotted spots.
coord.cols: Metadata coordinate columns used when no image is available.
flip.y: Reverse the y axis for metadata coordinates.
show_axes: Keep axis text, ticks, and grid when theme_use is "theme_spatial".
split.by: Metadata column to facet by.
cells: Cell names to include.
show_na: If TRUE, color NA groups with bg_color; if FALSE, drop them.
pt.size, pt.alpha: Point size and transparency. pt.size = NULL scales with sqrt(n) (minimum 0.3). Rasterized points keep at least a two-pixel radius at raster.dpi = c(512, 512) and scale with raster.dpi.
pie.radius, pie.radius.scale: Pie radius. NULL estimates from spot spacing, then multiplies by pie.radius.scale.
stroke: Point border width.
jitter_width, jitter_height: Jitter when geom = "jitter".
palette, palcolor: Palette name (thisplot::show_palettes) or custom colors.
bg_color: Point border color.
legend.position, legend.direction, legend.title: Legend placement ("none", "left", "right", "bottom", "top"), direction, and title. legend.title = NULL uses the group name.
theme_use: Theme name or function.
theme_args: Theme name or function, plus extra theme arguments.
combine, nrow, ncol, byrow: Combine plots with patchwork. combine = FALSE returns a list of ggplots.
verbose: Whether to print messages.
image.scale: Image scale factor matching the raster stored in the selected image. Use "hires" for a hires raster; do not modify Seurat scale-factor slots.

Value

A ggplot, patchwork, or list of ggplot objects.

Examples

data(visium_human_pancreas_sub)
SpatialSpotPlot(
  visium_human_pancreas_sub,
  group.by = "coda_label"
)


SpatialSpotPlot(
  visium_human_pancreas_sub,
  features = rownames(visium_human_pancreas_sub)[1:2],
  layer = "counts"
)