SpatialEcoTyper spatial plot

Plot SpatialEcoTyper labels on spatial coordinates using the spatial plotting style.

Usage

SpatialEcoTyperSpatialPlot(
  srt,
  group.by = "SpatialEcoTyper_SE",
  x.by = "X",
  y.by = "Y",
  image = NULL,
  overlay_image = TRUE,
  coord.cols = c(x.by, y.by),
  palette = "Paired",
  palcolor = NULL,
  theme_use = "theme_scop",
  ...,
  image.scale = c("lowres", "hires")
)

Arguments

srt

A Seurat object.

group.by

Metadata column containing SpatialEcoTyper labels.

x.by, y.by

Metadata coordinate columns used when no image coordinates are available.

image

Spatial image name. Required when multiple images are present; a single image is selected automatically when NULL.

overlay_image

Whether to draw the selected spatial image.

coord.cols

Metadata coordinate columns used when no image is available.

palette, palcolor

Palette passed to palette_colors().

theme_use

Theme name or function.

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.

...

Additional arguments passed to SpatialSpotPlot().

Value

A ggplot, patchwork, or list of ggplot objects.

Examples

counts <- matrix(
  c(3, 0, 1, 2, 0, 4, 1, 0, 2, 1, 3, 0),
  nrow = 3,
  byrow = TRUE
)
rownames(counts) <- c("EPCAM", "COL1A1", "PTPRC")
colnames(counts) <- paste0("spot", 1:4)
srt <- Seurat::CreateSeuratObject(counts)
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
srt$X <- c(0, 1, 0, 1)
srt$Y <- c(0, 0, 1, 1)
srt$SpatialEcoTyper_SE <- c("SE1", "SE1", "SE2", "SE2")
srt$CellType <- c("Epithelial", "Fibroblast", "Immune", "Epithelial")

SpatialEcoTyperSpatialPlot(
  srt,
  overlay_image = FALSE,
  coord.cols = c("X", "Y"),
  pt.size = 4
)