plot_map: Plot similarity map of single cells
In quadbiolab/VoxHunt: Projecting single-cell transcriptomes to spatial brain maps

plot_map

R Documentation

Plot similarity map of single cells

Description

Plot similarity map of single cells

Usage

plot_map(object, ...)

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

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

## S3 method for class '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.