Plot stored COMMOT results

Plot stored COMMOT group communication, cluster matrices, or raw-coordinate direction vectors without rerunning Python.

Usage

COMMOTPlot(
  object,
  result.name = NULL,
  plot_type = c("network", "matrix", "direction"),
  key = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  ...
)

Arguments

object

A `Seurat` object with COMMOT results.

result.name

Stored COMMOT result name.

plot_type

Network, cluster matrix, or direction-vector view.

key

Stored cluster or direction selection key.

theme_use, theme_args

Theme name or function, plus extra theme arguments. Applied to every plot type, including the network view.

...

Arguments passed to the SCOP network plot for `"network"`.

Value

A `ggplot` or compatible plot object.

Examples

if (FALSE) { # \dontrun{
data(visium_human_pancreas_sub)
spatial <- RunCOMMOT(
  visium_human_pancreas_sub,
  group.by = "CellType",
  coord.cols = c("col", "row"),
  cluster = TRUE,
  direction = TRUE,
  backend = "r"
)
COMMOTPlot(spatial, plot_type = "matrix")
COMMOTPlot(spatial, plot_type = "direction")
COMMOTPlot(spatial, plot_type = "network")
} # }