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Plot cells located within spatial boundaries or ring regions

Source: R/PlotCellsInside.R
PlotCellsInside.Rd

Visualizes cells that fall within defined spatial regions (boundaries or rings), typically obtained using the getCellsInside() function. The cells are colored by cluster, and the function offers two plotting modes: using geom_sf() (with fixed 1:1 aspect ratio) or geom_point() (with more flexible layout).

Usage

plotCellsInside(
  cells_inside = NULL,
  point_size = 0.5,
  colors = colors15_cheng,
  theme_ggplot = theme_spneigh(),
  legend_size = 2,
  fixed_aspect_ratio = TRUE
)

Arguments

cells_inside

An sf object of cells returned by getCellsInside(). Must contain cluster and region_id columns.

point_size

Numeric. Size of the points representing cells. Default is 0.5.

colors

A vector of cluster colors. Default uses colors15_cheng.

theme_ggplot

A ggplot2 theme object. Default is theme_spneigh().

legend_size

Numeric. Size of legend keys. Default is 2.

fixed_aspect_ratio

Logical. If TRUE, uses geom_sf() to preserve spatial scale. If FALSE, uses geom_point() with extracted coordinates. Default is TRUE.

Value

A ggplot object showing the cells colored by cluster within spatial regions.

Examples

coords <- readRDS(system.file("extdata", "MouseBrainCoords.rds",
    package = "SpNeigh"
))

# Obtain boundaries
boundary_points <- getBoundary(data = coords, one_cluster = 2)

# Select regions of interests if needed (Optional)
boundary_points <- subset(boundary_points, region_id == 2)

# Plot cells inside boundaries
cells_inside <- getCellsInside(data = coords, boundary = boundary_points)
plotCellsInside(cells_inside)


# Plot cells inside rings
ring_regions <- getRingRegion(boundary = boundary_points, dist = 100)
cells_ring <- getCellsInside(data = coords, boundary = ring_regions)
plotCellsInside(cells_ring, fixed_aspect_ratio = FALSE)