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
)

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.

assay

Assay used for features. If NULL, the default assay is used.

layer

Assay layer used for features.

image

Name of the Seurat spatial image. Required when multiple images are present; a single image is selected automatically when NULL.

overlay_image

Whether to draw the spatial image beneath spots.

image.alpha

Transparency of the spatial image.

coord.cols

Metadata coordinate columns used when no image is available.

flip.y

Whether to reverse the y axis for metadata coordinates.

pt.size

Point size.

pt.alpha

Point alpha.

stroke

Point border width.

palette

Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".

palcolor

Custom colors used to create a color palette. Default is NULL.

legend.position

The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".

theme_use

Theme used. Can be a character string or a theme function. Default is "theme_scop".

theme_args

Other arguments passed to the theme_use. Default is list().

combine

Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.

nrow

Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.

ncol

Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.

byrow

Whether to arrange the plots by row in the combined plot. Default is TRUE.

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")