Plot cell2location spatial results

Usage

Cell2locationPlot(
  srt,
  plot_type = c("proportion", "abundance", "dominant", "pie"),
  cell_types = NULL,
  prefix = "Cell2location",
  tool_name = "Cell2location",
  image = NULL,
  overlay_image = TRUE,
  coord.cols = c("col", "row"),
  ...,
  image.scale = c("lowres", "hires")
)

Arguments

srt: A Seurat object returned by RunCell2location().
plot_type: Result to draw: normalized proportion, q05 absolute abundance, dominant cell type, or a spot-level proportion pie.
cell_types: Optional cell types to display for abundance, proportion, or pie plots.
prefix: Metadata prefix used by RunCell2location().
tool_name: Name of the srt@tools result entry.
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.
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 plots.

Examples

if (FALSE) { # \dontrun{
# Result from the official Human Lymph Node example in RunCell2location().
spatial <- readRDS("human_lymph_node_cell2location/official_human_lymph_node.rds")
selected <- names(sort(
  colMeans(spatial@tools$Cell2location$proportions),
  decreasing = TRUE
))[1:6]
Cell2locationPlot(
  spatial,
  plot_type = "proportion",
  cell_types = selected,
  overlay_image = FALSE,
  coord.cols = c("x", "y"),
  ncol = 3
)
Cell2locationPlot(
  spatial,
  plot_type = "dominant",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)
} # }