Plot stored spatial deconvolution proportions

Plot spot-by-cell-type proportions stored by RunRCTD(), RunCARD(), RunSPOTlight(), or RunSpatialDWLS(). The plot reads a schema-v1 result through GetSpatialResult() and never reruns a deconvolution backend. RunCSIDE() is intentionally excluded because its output represents differential or context effects rather than cell-type proportions.

Usage

SpatialDeconvolutionPlot(
  srt,
  tool_name = NULL,
  cell_types = NULL,
  plot_type = c("point", "dominant", "pie"),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  ...
)

Arguments

srt

A spatial Seurat object containing a stored deconvolution result.

tool_name

Exact key in srt@tools. If NULL, exactly one compatible stored result must be discoverable.

cell_types

Optional cell types to display. The default uses all stored cell types.

plot_type

Plot proportions as separate point maps, one dominant-type map derived from the stored proportions, or one spot-level pie map.

combine

Whether to combine point maps. If FALSE, return a named list.

nrow, ncol, byrow

Point-map layout controls. When both dimensions are NULL, a near-square layout with at most three columns is used.

...

Additional arguments passed to SpatialSpotPlot().

Value

A ggplot, patchwork, or named list of ggplot objects.

Examples

data(visium_human_pancreas_sub)
data(pancreas_sub)
shared <- head(intersect(
  rownames(visium_human_pancreas_sub),
  rownames(pancreas_sub)
), 40)
spatial <- RunSpatialDWLS(
  visium_human_pancreas_sub[shared, 1:20],
  reference = pancreas_sub,
  reference_label = "CellType",
  features = shared,
  coord.cols = c("x", "y"),
  normalize = FALSE,
  verbose = FALSE
)
#> Warning: Not validating Centroids objects
#> Warning: Not validating Centroids objects
#> Warning: Not validating FOV objects
#> Warning: Not validating FOV objects
#> Warning: Not validating FOV objects
#> Warning: Not validating FOV objects
#> Warning: Not validating FOV objects
#> Warning: Not validating FOV objects
#> Warning: Not validating Seurat objects
SpatialDeconvolutionPlot(
  spatial,
  tool_name = "SpatialDWLS",
  cell_types = colnames(spatial@tools$SpatialDWLS$proportions)[1],
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)