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Plot STdeconvolve topic proportions

Source: R/RunSTdeconvolve.R
STdeconvolvePlot.Rd

Plot stored topic proportions without rerunning the optional backend. Multi-topic point maps use one shared proportion scale and reserve title space above the automatic layout.

Usage

STdeconvolvePlot(
  object,
  tool_name = "STdeconvolve",
  topics = NULL,
  prefix = NULL,
  plot_type = c("point", "pie"),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  ...,
  image.scale = c("lowres", "hires"),
  srt = NULL
)

Arguments

object

A Seurat object.

tool_name

Result key written to srt@tools by RunSTdeconvolve().

topics

Topic names, topic numbers, or metadata columns to plot. If NULL, all topics in the stored result are used.

prefix

Metadata prefix used by RunSTdeconvolve(). If NULL, the prefix is read from the stored result.

plot_type

"point" or "pie". Pie uses numeric group.by columns, values, or "<prefix>_prop_*"/"<prefix>_frac_*" when group.by is "<prefix>_dominant_type".

combine

Whether to combine point plots. If FALSE, a named list of plots is returned.

nrow, ncol, byrow

Point-plot layout controls. When both nrow and ncol are NULL, a near-square layout with at most three columns is used.

...

Additional arguments passed to SpatialSpotPlot().

image.scale

Image scale factor matching the raster stored in the selected image. Use "hires" for a hires raster; do not modify Seurat scale-factor slots.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A ggplot, patchwork, or list of ggplot objects.

See also

RunSTdeconvolve()