rliger (version 2.0.1)

plotSpatial2D: Visualize a spatial dataset

Description

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,
  ...
)

Value

A ggplot object

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.

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")