clusterPlot: Plot spatial cluster assignments.

In edward130603/BayesSpace: Clustering and Resolution Enhancement of Spatial Transcriptomes

Plot spatial cluster assignments.

Description

Plot spatial cluster assignments.

Usage

clusterPlot(
  sce,
  label = "spatial.cluster",
  palette = NULL,
  color = NULL,
  platform = NULL,
  is.enhanced = NULL,
  nsubspots.per.edge = 3,
  ...
)

Arguments

sce	SingleCellExperiment. If fill is specified and is a string, it must exist as a column in colData(sce).
label	Labels used to color each spot. May be the name of a column in colData(sce), or a vector of discrete values.
palette	Optional vector of hex codes to use for discrete spot values.
color	Optional hex code to set color of borders around spots. Set to NA to remove borders.
platform	Spatial sequencing platform. If "Visium", the hex spot layout will be used, otherwise square spots will be plotted. NOTE: specifying this argument is only necessary if sce was not created by spatialCluster() or spatialEnhance().
is.enhanced	True if sce contains subspot-level data instead of spots. Spatial sequencing platform. If true, the respective subspot lattice for each platform will be plotted. NOTE: specifying this argument is only necessary if sce was not created by spatialCluster() or spatialEnhance().
nsubspots.per.edge	Number of subspots per edge of the square. Only valid when platform is 'ST' or 'VisiumHD'.
...	Additional arguments for geom_polygon(). size, to specify the linewidth of these borders, is likely the most useful.

Value

Returns a ggplot object.

See Also

Other spatial plotting functions: featurePlot()

Examples

sce <- exampleSCE()
clusterPlot(sce)

edward130603/BayesSpace documentation built on Oct. 23, 2024, 7:04 a.m.