Plot spatial variable feature results

Visualize normalized results produced by RunSpatialVariableFeatures(). The summary view shows feature ranks and, when finite p- or q-values are stored, significance. Results without permutation statistics are shown without a significance size mapping or legend. The surface view reuses SpatialSpotPlot() to draw spatial expression for selected features.

Usage

SpatialVariableFeaturePlot(
  srt,
  plot_type = c("summary", "surface", "combined"),
  features = NULL,
  nfeatures = 10,
  score_col = "score",
  assay = NULL,
  layer = NULL,
  image = NULL,
  overlay_image = TRUE,
  image.alpha = 1,
  coord.cols = c("col", "row"),
  flip.y = TRUE,
  pt.size = NULL,
  pt.alpha = 0.9,
  stroke = 0.1,
  palette = "Spectral",
  palcolor = NULL,
  legend.position = "right",
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  image.scale = c("lowres", "hires")
)

Arguments

srt

A Seurat object.

plot_type

Plot type: "summary", "surface", or "combined".

features

Features to plot. If NULL, top features from the stored spatial variable feature result are used.

nfeatures

Number of top features used when features = NULL.

score_col

Result column used for the summary x-axis.

legend.position

Legend position for surface plots.

assay

Assay to use. NULL uses the default assay.

layer

Assay layer to use.

image

Spatial image name. Required when multiple images are present; a single image is selected automatically when NULL.

overlay_image, image.alpha

Draw the spatial image beneath spots.

coord.cols

Metadata coordinate columns used when no image is available.

flip.y

Reverse the y axis for metadata coordinates.

pt.size, pt.alpha

Point size and transparency. pt.size = NULL scales with sqrt(n) (minimum 0.3). Rasterized points keep at least a two-pixel radius at raster.dpi = c(512, 512) and scale with raster.dpi.

stroke

Point border width.

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.

combine, nrow, ncol, byrow

Combine plots with patchwork. combine = FALSE returns a list of ggplots.

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.

Value

A ggplot or patchwork object.

Examples

data(visium_human_pancreas_sub)
spatial <- Seurat::NormalizeData(
  visium_human_pancreas_sub,
  assay = "Spatial",
  verbose = FALSE
)
spatial <- RunSpatialVariableFeatures(
  spatial,
  assay = "Spatial",
  nfeatures = 10,
  verbose = FALSE
)
SpatialVariableFeaturePlot(spatial, plot_type = "summary")