Plot a subset of cells — plot_subpopulation • aquarius

A wrapper of the Seurat::DimPlot function to visualize a subset of cells, while other cells are represented as a background.

Usage

plot_subpopulation(
  sobj,
  reduction = "umap",
  identity = NULL,
  group_by = NULL,
  group_color = NULL,
  plot_title = NULL,
  bg_color = "gray92",
  name_other = "other",
  ...
)

Arguments

sobj: A Seurat object
reduction: CHARACTER : name of a reduction present in the Seurat object (default to 'umap')
identity: CHARACTER VECTOR: in Seurat::Idents(sobj), the specific identities to display (default to the first one)
group_by: CHARACTER : name of a column in sobj@metadata, to group cells by (default to the identities)
group_color: CHARACTER : named vector of colors for the levels of group_color, to color cells (default to ggplot default colors)
plot_title: CHARACTER : plot title (default to NULL)
bg_color: CHARACTER : background colors (default to "gray92")
name_other: CHARACTER : name associated with the background (default to "other")
...: other values passed to the Seurat::DimPlot function

Value

A ggplot object