Feature plot over an embedding — feature_plot

Plots the expression of one or more features over an embedding. By default every feature gets its own panel and its own colour bar (scale_mode = "free"), so a weakly expressed gene is not flattened by whatever the loudest gene in the set happens to be. Use scale_mode = "shared" for a single faceted plot with one colour bar across all features.

Usage

feature_plot_sc(
  object,
  features,
  embedding,
  feature_labels = NULL,
  scale = FALSE,
  clip = NULL,
  expr_modality = c("rna", "adt"),
  embd_modality = c("rna", "adt", "wnn"),
  point_size = NULL,
  point_alpha = 0.5,
  raster = NULL,
  raster_dpi = c(512, 512),
  label_by = NULL,
  label_size = 3,
  label_color = "black",
  label_font = "bold",
  highlight_features = FALSE,
  highlight_quantile = 0.25,
  scale_mode = c("free", "shared"),
  palette = c("sequential", "spectral", "viridis", "diverging"),
  ncol = NULL,
  ...
)

Arguments

object: A single cell class.
features: Character vector. Gene/feature IDs to plot, taken from expr_modality.
embedding: String. Name of the embedding.
feature_labels: Optional named character vector mapping gene ids to display labels (default: NULL).
scale: Boolean. Whether to z-score the expression values.
clip: Optional numeric. Clip z-scores if scale = TRUE.
expr_modality: String. Modality the expression is pulled from. One of c("rna", "adt").
embd_modality: String. Modality the embedding is pulled from. One of c("rna", "adt", "wnn"). Use "wnn" for WNN-derived embeddings.
point_size: Optional numeric. Defines the point size. If not provided, will be auto-determined.
point_alpha: Numeric. Defines the alpha.
raster: Optional boolean. Shall the plot be rasterised. If NULL and number of cells is larger than 1e5, defaults to TRUE.
raster_dpi: Two numerics. Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
label_by: String. Optional obs column to label by. (default: NULL).
label_size: Numeric. Size of the labels
label_color: String. Color fo the labels.
label_font: String. Font of the labels.
highlight_features: Boolean. Shall the features be more strongly highlighted. Useful for sparsely expressed genes.
highlight_quantile: Numeric between [0, 1]. Defines the threshold.
scale_mode: String. One of c("free", "shared"). With "free" each feature is drawn as its own plot with its own colour bar and the panels are combined with patchwork::wrap_plots(). With "shared" all features go into one faceted plot with a single colour bar fitted to the pooled expression.
palette: String. Continuous palette for the expression values. One of c("sequential", "spectral", "viridis", "diverging"), see bx_colors().
ncol: Optional integer. Number of columns of the panel grid. Only has an effect if scale_mode = "free". If NULL, patchwork picks the layout.
...: Additional arguments forwarded to bixverse::extract_feature_plot_data() and onward to get_embedding(). Do not pass modality here; use embd_modality instead.

Value

A patchwork object if scale_mode = "free", otherwise a ggplot object.