Plot similarity map of single cells

plot_map(object, ...)

# S3 method for VoxelMap
plot_map(
  object,
  view = c("sagittal", "coronal", "traverse", "z", "x", "y", "slice", "3D"),
  slices = NULL,
  groups = NULL,
  annotation_level = "custom_2",
  annotation_colors = NULL,
  map_colors = gyrdpu_flat,
  show_coordinates = FALSE,
  show_legend = FALSE,
  ...
)

# S3 method for BrainSpanMap
plot_map(object, groups = NULL, map_colors = blues, scale = FALSE)

# S3 method for MousebrainMap
plot_map(
  object,
  groups = NULL,
  map_colors = ylorrd_flat,
  point_size = 0.2,
  subsample = 50000,
  scale = TRUE,
  show_legend = FALSE,
  ...
)

# S3 method for ReferenceMap
plot_map(
  object,
  groups = NULL,
  map_colors = ylorrd_flat,
  point_size = 0.2,
  subsample = NULL,
  scale = TRUE,
  show_legend = FALSE,
  ...
)

Arguments

...	Other arguments passed to patchwork::wrap_plots().
view	String indicating the perspective to show. Valid values are 'sagittal', 'coronal', 'traverse', 'z' , 'x', 'y', 'slice', '3D'.
slices	A numeric vector indicating the slices to plot.
groups	A metadata column or character vector to group the cells, e.g. clusters, cell types.
annotation_level	The structure annotation level to summarize to.
annotation_colors	Color map for structure annotation.
map_colors	Color map for correlation values.
show_coordinates	Logical. Whether to show slice coordinates or not.
show_legend	Logical. Whether to show a color legend or not.
scale	Logical. Whether to scale correlation values.
point_size	Point size.
subsample	Subsample reference cells for faster plotting.

Value

A similarity map.