Plot a graph produced by [RunSpatialNetwork()]. The graph can be read from a Seurat object or supplied directly as `srt@tools$SpatialNetwork`.
Usage
SpatialNetworkPlot(
object = NULL,
res = NULL,
graph.name = NULL,
group.by = NULL,
edge.color = "grey80",
edge.linewidth = 0.2,
pt.size = NULL,
pt.alpha = 1,
palette = "Paired",
palcolor = NULL,
raster = FALSE,
raster.dpi = 300,
theme_use = "theme_scop",
theme_args = list()
)Arguments
- object
Optional `Seurat` object containing the graph and metadata.
- res
Optional plain result list from `object@tools$SpatialNetwork`.
- graph.name
Stored graph name. The active graph is used when `NULL`.
- group.by
Node column or Seurat metadata column used for coloring.
- edge.color, edge.linewidth
Edge appearance.
- pt.size, pt.alpha
Node appearance.
- palette, palcolor
Palette name or explicit colors.
- raster
Whether to rasterize only the node layer.
- raster.dpi
Node rasterization resolution.
- theme_use, theme_args
scop theme and its arguments.