Violin Plot with ggbetweenstats-Style Aesthetics

Creates publication-ready violin plots for one or more features from a Seurat object, with optional boxplot overlay, jittered raw data points, and centrality markers (median/mean diamond with numeric label).

For a single feature, returns a bare ggplot2 object. For multiple features, returns a patchwork composition.

Usage

do_ViolinPlot(
  object,
  features,
  group.by = NULL,
  layer = "data",
  assay = NULL,
  colors.use = NULL,
  pt.size = 3,
  pt.alpha = 0.4,
  violin.alpha = 0.2,
  violin.width = 0.5,
  boxplot = TRUE,
  boxplot.width = 0.3,
  boxplot.alpha = 0.2,
  centrality = TRUE,
  centrality.fn = "median",
  ncol = NULL
)

Arguments

object: Seurat object.
features: character. Gene names or numeric metadata column names to plot (required). Can mix both types freely — each gets its own panel. Examples: c("CD3D", "nCount_RNA", "percent.mt").
group.by: character. Metadata column for grouping. If NULL (default), uses active Idents.
layer: character. Layer to extract expression from (default: "data"). Only applies to gene features.
assay: character. Assay to use (default: NULL = DefaultAssay).
colors.use: character. Named vector of colors for groups. If NULL, generates colors automatically with generate_badranseq_colors.
pt.size: numeric. Jitter point size (default: 3).
pt.alpha: numeric. Jitter point transparency (default: 0.4).
violin.alpha: numeric. Violin fill alpha (default: 0.2).
violin.width: numeric. Violin width (default: 0.5).
boxplot: logical. Whether to overlay a boxplot (default: TRUE).
boxplot.width: numeric. Boxplot width (default: 0.3).
boxplot.alpha: numeric. Boxplot alpha (default: 0.2).
centrality: logical. Whether to show centrality point and label (default: TRUE).
centrality.fn: character. Centrality function ("median" or "mean", default: "median").
ncol: numeric. Number of columns for patchwork layout when plotting multiple features (default: NULL = auto).

Value

A ggplot2 object (single feature) or patchwork object (multiple features).

Examples

if (FALSE) { # \dontrun{
# Single gene violin plot
do_ViolinPlot(seurat_obj, features = "CD3D")

# Multiple genes
do_ViolinPlot(seurat_obj, features = c("CD3D", "CD8A", "CD14"))

# Custom grouping and colors
do_ViolinPlot(seurat_obj, features = "CD3D",
              group.by = "seurat_clusters",
              colors.use = c("0" = "red", "1" = "blue"))

# Without boxplot and centrality
do_ViolinPlot(seurat_obj, features = "CD3D",
              boxplot = FALSE, centrality = FALSE)
} # }