plot_annotation: Plot brain structure annotation

In quadbiolab/VoxHunt: Projecting single-cell transcriptomes to spatial brain maps

Plot brain structure annotation

Description

Plot the voxel map of the developing mouse brain colorcoded by structure annotation.

Usage

plot_annotation(object = "E13", ...)

## Default S3 method:
plot_annotation(
  object = "E13",
  annotation_level = "custom_2",
  annotation_colors = NULL,
  slices = NULL,
  show_coordinates = FALSE,
  show_legend = FALSE,
  alpha = 0.5,
  class_colors = many,
  region_colors = mb_colors,
  point_size = 0.2,
  subsample = 50000
)

## S3 method for class 'VoxelMap'
plot_annotation(
  object,
  annotation_level = "custom_2",
  annotation_colors = NULL,
  slices = NULL,
  show_coordinates = FALSE,
  show_legend = FALSE,
  alpha = 0.5
)

## S3 method for class 'MousebrainMap'
plot_annotation(
  object,
  class_colors = many,
  region_colors = mb_colors,
  point_size = 0.2,
  subsample = 50000,
  show_legend = TRUE
)

Arguments

object	String indicating the developmental stage from the ABA.
...	Other arguments passed to patchwork::wrap_plots().
annotation_level	The structure annotation level to color code.
annotation_colors	A character vector with the color scale.
slices	A numeric vector indicating the slices to plot.
show_coordinates	Logical. Whether to show slice coordinates or not.
show_legend	Logical. Whether to show a color legend or not.
alpha	Float. The alpha value for grid tiles.
class_colors	Color map for classes (celltypes).
region_colors	Color map for regions.
point_size	Point size.
subsample	Subsample mousebrain cells for faster plotting.
groups	A metadata column or character vector to group the cells, e.g. clusters, cell types.
scale	Logical. Whether to scale correlation values.

Value

An annotation plot.

A similarity map.

quadbiolab/VoxHunt documentation built on March 4, 2024, 6:37 a.m.