Generalized Dimensionality Reduction Plot — do

Unified wrapper for dimensionality reduction plots. Routes to specialized functions for PCA and UMAP, handles other reductions directly. When split.by is used, shows each split category with a grey silhouette of all other cells.

Usage

do_DimPlot(
  object,
  reduction = "umap",
  dims = c(1, 2),
  group.by = NULL,
  split.by = NULL,
  colors.use = NULL,
  label = TRUE,
  label.size = 4,
  label.color = "black",
  label.fill = "white",
  pt.size = 1,
  pt.alpha = 1,
  plot.axes = TRUE,
  variance_digits = 1,
  shuffle = TRUE,
  plot_cell_borders = TRUE,
  border.size = 2,
  border.color = "black",
  legend.title = NULL,
  show.legend = TRUE,
  ncol = NULL,
  nrow = NULL,
  ...
)

Arguments

object: Seurat object.
reduction: character. Reduction to use (default: "umap").
dims: numeric. Vector of 2 PC dimensions to plot (default: c(1, 2)).
group.by: character. One or more metadata columns for grouping. If NULL (default), uses active Idents. When multiple columns are provided, each gets its own panel combined via patchwork.
split.by: character. Metadata column for splitting (creates panels with silhouettes).
colors.use: Named vector of colors for groups.
label: logical. Show cluster labels (default: TRUE).
label.size: numeric. Label font size (default: 4).
label.color: character. Label text color (default: "black").
label.fill: character. Label background fill (default: "white").
pt.size: numeric. Point size (default: 1).
pt.alpha: numeric. Point transparency (default: 1).
plot.axes: logical. Show axes (default: TRUE).
variance_digits: numeric. Decimal places for variance (default: 1).
shuffle: logical. Randomize cell plotting order (default: TRUE).
plot_cell_borders: logical. Plot black borders around cells (default: TRUE).
border.size: numeric. Border size multiplier (default: 2).
border.color: character. Border color (default: "black").
legend.title: character. Custom legend title (NULL removes title).
show.legend: logical. Show the colour legend (default: TRUE). Set to FALSE to hide the legend entirely.
ncol: numeric. Number of columns for panel layout (default: NULL, auto). Controls layout of both split panels and multi-column group.by panels.
nrow: numeric. Number of rows for panel layout (default: NULL, auto).
...: Additional arguments (currently unused).

Value

ggplot2 object with dimensionality reduction plot.

Examples

if (FALSE) { # \dontrun{
do_DimPlot(seurat_object, group.by = "condition")
do_DimPlot(seurat_object, reduction = "pca", group.by = "cluster")
do_DimPlot(seurat_object, split.by = "sample")  # Shows silhouettes
} # }