Spatial spot plot

Usage

SpatialSpotPlot(
  srt,
  group.by = NULL,
  features = NULL,
  assay = NULL,
  layer = "data",
  values = NULL,
  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,
  split.by = NULL,
  cells = NULL,
  show_na = FALSE,
  pt.size = NULL,
  pt.alpha = 0.9,
  stroke = 0.1,
  jitter_width = 0.25,
  jitter_height = 0.25,
  palette = ifelse(is.null(features), "Chinese", "Spectral"),
  palcolor = NULL,
  bg_color = "grey20",
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE
)

Arguments

srt: A Seurat object.
group.by: Metadata columns to color spots by.
features: Features to color spots by. When provided, expression values are read from assay and layer.
assay: Assay used for features. If NULL, the default assay is used.
layer: Assay layer used for features.
values: Optional vector, matrix, or data.frame with spot-level values. Row names or vector names must match spatial spot names.
plot.data: Optional long-format data.frame for plotting repeated spatial points, such as cell-to-spot assignments.
spot.by: Column in plot.data containing spot names.
color.by: Column in plot.data used to color repeated spatial points.
geom: Geometry used for plot.data: "point" or "jitter".
image: Name of the Seurat spatial image. If NULL, the first image is used when present.
overlay_image: Whether to draw the spatial image beneath spots.
image.alpha: Transparency of the spatial image.
crop: Whether to crop the panel to plotted spots.
coord.cols: Metadata coordinate columns used when no image is available.
flip.y: Whether to reverse the y axis for metadata coordinates.
split.by: Name of a column in meta.data column to split plot by. Default is NULL.
cells: A character vector of cell names to use.
show_na: Whether to assign a color from the color palette to NA group. If TRUE, cell points with NA level will be colored by bg_color. If FALSE, cell points with NA level will be removed from the plot.
pt.size: Point size.
pt.alpha: Point alpha.
stroke: Point border width.
jitter_width, jitter_height: Jitter size used when geom = "jitter".
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".
palcolor: Custom colors used to create a color palette. Default is NULL.
bg_color: Point border color.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
legend.title: Title for the legend. Default is NULL, which uses the group name.
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
combine: Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow: Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
ncol: Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
byrow: Whether to arrange the plots by row in the combined plot. Default is TRUE.

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"
)