Plot a dot plot with categorical groups — sn_plot

This function plots a dot plot with categorical groups using the DotPlot function from the Seurat package.

Usage

sn_plot_dot(
  x,
  assay = NULL,
  features,
  de_name = "default",
  n = 3,
  marker_groups = NULL,
  col_min = -2.5,
  col_max = 2.5,
  dot_min = 0,
  dot_scale = 4,
  idents = NULL,
  group_by = NULL,
  split_by = NULL,
  cluster_idents = FALSE,
  scale = TRUE,
  scale_by = "radius",
  scale_min = NA,
  scale_max = NA,
  palette = "RdBu"
)

Arguments

x: A Seurat object containing the data to plot.
assay: The assay to plot. Defaults to the default assay.
features: A character vector of feature names to plot, or "top_markers" to automatically use the top stored DE markers from object@misc$de_results[[de_name]].
de_name: Name of the stored DE result to use when features = "top_markers". Defaults to "default".
n: Number of genes to select per group when features = "top_markers". Defaults to 3.
marker_groups: Optional subset of DE result groups to include when features = "top_markers".
col_min: The minimum value for the color scale. Defaults to -2.5.
col_max: The maximum value for the color scale. Defaults to 2.5.
dot_min: The minimum value for the dot size scale. Defaults to 0.
dot_scale: The size of the dots to plot.
idents: A character vector of identities to plot. Defaults to all identities.
group_by: A character vector specifying the grouping variable. Defaults to "ident".
split_by: A character vector specifying the splitting variable.
cluster_idents: Whether to cluster the identities or not. Defaults to FALSE.
scale: Whether to scale the dot size or not. Defaults to TRUE.
scale_by: The variable to scale the dot size by. Defaults to "radius".
scale_min: The minimum value for the dot size scale. Defaults to NA.
scale_max: The maximum value for the dot size scale. Defaults to NA.
palette: The diverging palette used for the color scale.

Value

A ggplot2 object.

Examples

if (FALSE) { # \dontrun{
sn_plot_dot(x = mySeuratObject, features = c("CD3D", "CD8A", "CD4"))
} # }