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Plot Feature Dispersion

plot_feature_dispersion.Rd

This function generates a scatter plot comparing feature expression levels to their variability (dispersion). It supports objects from both Monocle3 (cell_data_set) and Seurat. If feature selection has been performed (i.e., use_for_ordering is present in the dispersion metadata), selected features are highlighted in red ("firebrick1"), while others are shown in gray.

Usage

plot_feature_dispersion(cds, size = 1, alpha = 0.4)

Arguments

cds

An object of class cell_data_set (Monocle3) or Seurat. The object must have dispersion data pre-calculated and stored in:

  • cds@int_metadata$dispersion for cell_data_set objects.

  • cds@misc$dispersion for Seurat objects.

size

Numeric. The size of the points in the scatter plot. Default is 1.

alpha

Numeric. The transparency level of the points, ranging from 0 (invisible) to 1 (solid). Default is 0.4.

Value

A ggplot object representing the dispersion plot. This allows further modification using standard ggplot2 functions (e.g., adding titles or changing themes).

Details

Visualizes the relationship between the log mean expression and log dispersion of features (genes) in a single-cell dataset.

Examples

if (FALSE) { # \dontrun{
  # For a Monocle3 object
  p <- plot_feature_dispersion(cds, size = 1.5, alpha = 0.5)
  p + ggplot2::ggtitle("Dispersion Plot")

  # For a Seurat object
  # Ensure dispersion is calculated and stored in @misc$dispersion first
  p_seurat <- plot_feature_dispersion(seurat_obj)
} # }