Visualize a spatial dataset

Usage

plotSpatial2D(object, ...)

# S3 method for liger
plotSpatial2D(object, dataset, useCluster = NULL, legendColorTitle = NULL, ...)

# S3 method for ligerSpatialDataset
plotSpatial2D(
  object,
  useCluster = NULL,
  legendColorTitle = NULL,
  useDims = c(1, 2),
  xlab = NULL,
  ylab = NULL,
  labelText = FALSE,
  ...
)

Arguments

object: Either a liger object containing a spatial dataset or a ligerSpatialDataset object.
...: Arguments passed to other methods. .liger method passes everything to .ligerSpatialDataset method, and the latter passes everything to .ggScatter and then .ggplotLigerTheme.
dataset: Name of one spatial dataset.
useCluster: Either the name of one variable in cellMeta(object) or a factor object with annotation that matches with all cells in the specified dataset. Default NULL uses default clusters.
legendColorTitle: Alternative title text in the legend. Default NULL uses the variable name set by useCluster, or "Annotation" is useCluster is a customized factor object.
useDims: Numeric vector of two, choosing the coordinates to be drawn on 2D space. (STARmap data could have 3 dimensions.) Default c(1, 2).
xlab, ylab: Text label on x-/y-axis. Default NULL does not show it.
labelText: Logical, whether to label annotation onto the scatter plot. Default FALSE.

Value

A ggplot object

Examples

ctrl.fake.spatial <- as.ligerDataset(dataset(pbmc, "ctrl"), modal = "spatial")
fake.coords <- matrix(rnorm(2 * ncol(ctrl.fake.spatial)), ncol = 2)
dimnames(fake.coords) <- list(colnames(ctrl.fake.spatial), c("x", "y"))
coordinate(ctrl.fake.spatial) <- fake.coords
dataset(pbmc, "ctrl") <- ctrl.fake.spatial
plotSpatial2D(pbmc, dataset = "ctrl")