Plot cellspec quality-control views

Draws a centroid map, marker distribution, feature-support heatmap, cell area distribution, or an overview of up to four panels. The overview leaves out the area panel when the cells table has no area column and the marker panel when there are no intensity features. Large objects are subsampled deterministically for plotting.

Usage

# S3 method for class 'cellspec'
plot(
  x,
  type = c("overview", "map", "marker", "support", "area"),
  colour_by = NULL,
  marker = NULL,
  policy = NULL,
  max_points = 50000L,
  seed = 1L,
  ...
)

Arguments

x

A cellspec object.

type

Plot type: "overview", "map", "marker", "support" or "area".

colour_by

A cells or measurement column used by the map.

marker

Marker used by the marker plot.

policy

Optional signal policy for the marker plot.

max_points

Maximum number of cells used by a plot.

seed

Seed used for deterministic subsampling.

...

Reserved for future plot-specific parameters.

Value

A ggplot object, or a patchwork object for type = "overview".

See also

Other methods: [.cellspec(), as.data.frame.cellspec(), cellspec-methods

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot(cs_example(), type = "map")
}