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Plot spatial integration results

Source: R/RunSpatialIntegration.R
SpatialIntegrationPlot.Rd

Visualize standardized results produced by RunSpatialIntegration().

Usage

SpatialIntegrationPlot(
  object,
  method = NULL,
  plot_type = c("spatial", "embedding", "alignment", "composition"),
  group.by = NULL,
  sample.by = NULL,
  reduction = NULL,
  cluster_colname = NULL,
  coord.cols = c("col", "row"),
  use_aligned = FALSE,
  tool_name = "SpatialIntegration",
  combine = TRUE,
  palette = "Chinese",
  palcolor = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  ...,
  image.scale = c("lowres", "hires"),
  srt = NULL
)

Arguments

object

A Seurat object containing spatial integration results.

method

Stored integration method. If NULL, the active method stored in srt@tools[[tool_name]] is used.

plot_type

Plot type: "spatial", "embedding", "alignment", or "composition".

group.by

Metadata column used for coloring. Defaults to the stored spatial domain column.

sample.by

Metadata column used for facets or composition grouping. Defaults to the stored sample column.

reduction

Reduction used for embedding plots. Defaults to the stored integration reduction.

cluster_colname

Backward-compatible alias for group.by.

coord.cols

Metadata coordinate columns used when no image is available.

use_aligned

Whether spatial plots should use aligned coordinates when available.

tool_name

Name of the srt@tools entry created by RunSpatialIntegration().

combine

Whether to combine plots when delegated plotting returns a list.

palette, palcolor

Palette name (thisplot::show_palettes) or custom colors.

theme_use

Theme name or function.

theme_args

Theme name or function, plus extra theme arguments.

...

Additional arguments passed to SpatialSpotPlot() or CellDimPlot(). For spatial maps, image can be one image or a named sample-to-image vector using names in the merged object. By default, each sample uses its uniquely matching image. nrow, ncol and byrow control the layout of separate image panels.

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 object, or list of plots.

Details

Raw spatial maps retain every sample and use consistent category colors. Aligned maps use the stored aligned coordinates without a raw tissue-image overlay. This plotting option does not perform image registration.

See also

RunSpatialIntegration()

Examples

if (FALSE) { # \dontrun{
# Template: visium_S1 and visium_S2 are existing spatial Seurat samples.
spatial <- RunSpatialIntegration(
  list(S1 = visium_S1, S2 = visium_S2),
  method = "PRECAST",
  assay = "Spatial",
  image = c(S1 = "slice1", S2 = "slice1")
)
SpatialIntegrationPlot(spatial, method = "PRECAST", plot_type = "spatial")
} # }