Plot spatial integration results

Visualize standardized results produced by RunSpatialIntegration().

Usage

SpatialIntegrationPlot(
  srt,
  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")
)

Arguments

srt

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.

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.

...

Additional arguments passed to SpatialSpotPlot() or CellDimPlot().

Value

A ggplot, patchwork object, or list of plots.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial$sample <- ifelse(spatial$y > stats::median(spatial$y), "slice_a", "slice_b")
spatial$SpatialIntegration_PRECAST_domain <- factor(
  paste0("domain_", (seq_len(ncol(spatial)) - 1) %% 3 + 1)
)
embedding <- cbind(
  SI_1 = as.numeric(scale(spatial$x)),
  SI_2 = as.numeric(scale(spatial$y))
)
rownames(embedding) <- colnames(spatial)
spatial[["SpatialIntegration_PRECAST"]] <- SeuratObject::CreateDimReducObject(
  embeddings = embedding,
  key = "SI_",
  assay = "Spatial"
)
spatial$SpatialIntegration_PRECAST_aligned_x <- spatial$x +
  ifelse(spatial$sample == "slice_b", -stats::median(spatial$x), 0)
spatial$SpatialIntegration_PRECAST_aligned_y <- spatial$y
integration_parameters <- list(
  method = "PRECAST",
  sample.by = "sample",
  assay = "Spatial",
  layer = "counts",
  coord.cols = c("x", "y"),
  reduction.name = "SpatialIntegration_PRECAST",
  cluster_colname = "SpatialIntegration_PRECAST_domain",
  aligned_coord_cols = c(
    "SpatialIntegration_PRECAST_aligned_x",
    "SpatialIntegration_PRECAST_aligned_y"
  )
)
spatial@tools$SpatialIntegration <- list(
  active_method = "PRECAST",
  methods = list(PRECAST = list(parameters = integration_parameters)),
  parameters = integration_parameters,
  samples = unique(spatial$sample),
  cells = colnames(spatial)
)

SpatialIntegrationPlot(
  spatial,
  plot_type = "spatial",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)
#> Error in spatial_require_coordinate_contract(method_bundle, "RunSpatialIntegration()"): Stored spatial result uses an old or unknown coordinate contract; rerun
#> RunSpatialIntegration() with the current SCOP version
SpatialIntegrationPlot(spatial, plot_type = "embedding")
#> Error in spatial_require_coordinate_contract(method_bundle, "RunSpatialIntegration()"): Stored spatial result uses an old or unknown coordinate contract; rerun
#> RunSpatialIntegration() with the current SCOP version
SpatialIntegrationPlot(spatial, plot_type = "alignment")
#> Error in spatial_require_coordinate_contract(method_bundle, "RunSpatialIntegration()"): Stored spatial result uses an old or unknown coordinate contract; rerun
#> RunSpatialIntegration() with the current SCOP version
SpatialIntegrationPlot(spatial, plot_type = "composition")
#> Error in spatial_require_coordinate_contract(method_bundle, "RunSpatialIntegration()"): Stored spatial result uses an old or unknown coordinate contract; rerun
#> RunSpatialIntegration() with the current SCOP version