Dot plot of marker gene expression across groups

Usage

dot_plot_sc(
  object,
  features,
  grouping_variable,
  feature_labels = NULL,
  feature_grouping = NULL,
  scale_exp = TRUE,
  modality = c("rna", "adt"),
  cluster_groups = TRUE,
  palette = c("sequential", "spectral", "viridis", "diverging")
)

Arguments

object: A single cell class.
features: Character vector. Gene IDs to plot.
grouping_variable: String. Obs column to group by.
feature_labels: Optional named character vector mapping gene ids to display labels (default: NULL).
feature_grouping: Optional named character vector mapping gene ids to grouping labels, e.g. cell type labels. If feature_labels is provided, the character vectors should contain the mapping of feature display labels to their respecitve groups (e.g. c(CD3E = "T cell", CD8A = "T cell", MS4A1 = "B cell", ...). (default: NULL).
scale_exp: Boolean. Whether to min-max scale mean expression per gene.
modality: String. One of c("rna", "adt").
cluster_groups: Boolean. Use hierarchical clustering on the grouping variable to re-order the group labels based on expression similarity.
palette: String. Continuous palette for the scaled expression. One of c("sequential", "spectral", "viridis", "diverging"), see bx_colors().

Value

A ggplot object.