Skip to contents

FeaturePlot

Source: R/FeaturePlot.R
FeaturePlot.Rd

Plot spatial gene expression. This function is a modified version of the featurePlot function from `BayesSpace` R package. In comparison to the original BayesSpace function, this function allows plotting multiple genes simultaneously and drawing an outline around a specified cluster. To draw outlines, the reconstructShapeDensityImage function from the `sosta` R package has been adapted. Compared to the original `sosta` function, this version allows the use of a SingleCellExperiment object, which cannot be used with `spatialCoords()`.

Usage

FeaturePlot(
  spe,
  feature,
  coordinates = NULL,
  concave_hull = FALSE,
  sf_dim = 200,
  assay.type = "logcounts",
  annotation_cluster = FALSE,
  annotation_title = NULL,
  platform = "Visium",
  cluster_col = NULL,
  cluster = NULL,
  legend_cluster = FALSE,
  legend_exprs = FALSE,
  diverging = FALSE,
  low = NULL,
  high = NULL,
  mid = NULL,
  color = NULL,
  linewidth = 0.4,
  linecolor = NULL,
  label = FALSE,
  ncol = 3,
  title = FALSE,
  title_size = 10,
  point_size = 0.5
)

Arguments

spe

SpatialExperiment or SingleCellExperiment. If feature is specified and is a string, it must exist as a row in the specified assay of spe.

feature

Feature vector used to color each cell. May be the name of a gene/row in an assay of spe, or a vector of continuous values.

coordinates

Column names for the spatial coordinates of cells stored in colData(spe). If specified, these coordinates will be used. If not, the function defaults to using 'row' and 'col' in colData(spe) if they exist. Otherwise, it will use spatialCoords(spe) if 'spe' is a SpatialExperiment object and spatialCoords(spe) is not NULL.

concave_hull

A logical value (TRUE or FALSE). For Visium or ST platforms, `concave_hull` is automatically set to TRUE. If TRUE, the function uses geom_mark_hull to outline cluster boundaries (recommended for non-discontinuous clusters). If FALSE, the adapted reconstructShapeDensityImage is used for complex cluster shapes.

sf_dim

A numeric value for the x-dimension of the reconstruction (default is 200). A lower value speeds up computation but reduces accuracy. Used only when `concave_hull` is FALSE.

assay.type

String indicating which assay in spe the expression vector should be taken from.

annotation_cluster

A logical value. TRUE or FALSE. If TRUE, annotated spatial clusters are plotted alongside expression plots. If FALSE, clusters are not displayed.

annotation_title

A character string for the title of the annotated spatial clusters. Applied only when `annotation_cluster` is TRUE.

platform

A character string specifying the spatial sequencing platform. If "Visium" or "ST", a hexagonal spot layout will be used. Otherwise, points will be plotted.

cluster_col

Column name of spatial clusters in colData(spe).

cluster

Names of the spatial clusters used for drawing a boundary around a group of points that belong to the specify cluster. It can be NULL, "all"/"ALL", or a vector of cluster names.

legend_cluster

A logical value. TRUE of FALSE, indicating whether to plot the legend for the shaped clusters (TRUE), or not (FALSE). Only used when 'cluster_col' and 'cluster' are specified, and is supported only when 'concave_hull' is set to TRUE.

legend_exprs

A logical value. TRUE of FALSE, indicating whether to plot the legend for the expression level (TRUE), or not (FALSE).

diverging

A logical value. If TRUE, uses a diverging color gradient in FeaturePlot (e.g., for fold change). If FALSE, uses a sequential gradient (e.g., for expression).

low, mid, high

Optional hex codes for low, mid, and high values of the color gradient used for continuous cell values.

color

Optional hex code to set color of borders around cells. Set to NA to remove borders.

linewidth

The width of the boundary line around the cluster. The default ('0.4') size of the boundary line is one.

linecolor

The colors of the boundary lines around the cluster. If unspecified, the default color scheme is used.

label

A logical. TRUE of FALSE. Adding a label and an arrow pointing to a group.

ncol

The dimensions of the grid to create. By default, 1, if the length of feature equals to 1, and 3, otherwise.

title

A logical. TRUE or FALSE. If true, the title name of each (subplot) is the gene name.

title_size

Title font size.

point_size

Point size.

Value

Returns a ggplot object.

See also

svg_test, individual_svg, top_results, dsp_test, individual_dsp

Examples

# load the input data:
data("LIBD_subset", package = "DESpace")

# load pre-computed results (obtained via `svg_test`)
data("results_svg_test", package = "DESpace")

# Visualize the gene expression of the top three genes
feature = results_svg_test$gene_results$gene_id[seq_len(3)]
FeaturePlot(LIBD_subset, feature, coordinates = c("array_row", "array_col"),
            ncol = 3, title = TRUE)