do_ViolinPlot() | Distribution comparison

Violin plots show the full distribution shape of gene expression across groups. They combine the benefits of box plots and kernel density plots.

Basic usage

p <- SCpubr::do_ViolinPlot(sample = sample,
                           features = "nFeature_RNA",
                           group.by = "subtype")
p

Multiple features

p <- SCpubr::do_ViolinPlot(sample = sample,
                           features = c("nCount_RNA", "nFeature_RNA"),
                           group.by = "subtype",
                           ncol = 2)
p

Share Y-axis limits

Force all features to use the same Y-axis range:

p <- SCpubr::do_ViolinPlot(sample = sample,
                           features = c("nCount_RNA", "nFeature_RNA"),
                           group.by = "subtype",
                           ncol = 2,
                           share.y.lims = TRUE)
p

Show/hide boxplot

# Without boxplot
p <- SCpubr::do_ViolinPlot(sample = sample,
                           features = "nCount_RNA",
                           group.by = "subtype",
                           plot_boxplot = FALSE)
p

Split by variable

p <- SCpubr::do_ViolinPlot(sample = sample,
                           features = "nCount_RNA",
                           group.by = "subtype",
                           split.by = "technology",
                           plot_boxplot = FALSE,
                           order = FALSE)
p

Cut Y-axis

Truncate the Y-axis at a specific value:

p <- SCpubr::do_ViolinPlot(sample = sample,
                           features = "nCount_RNA",
                           group.by = "subtype",
                           y_cut = 25000)
p

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling, grid), see Shared features.

Core parameters

Parameter Description Default
features Features to plot —

Appearance

Parameter Description Default
plot_boxplot Show inner boxplot TRUE
boxplot_width Width of inner boxplot 0.2
line_width Violin border width 0.5
y_cut Y-axis cutoff per feature NA

Layout

Parameter Description Default
ncol Columns for multiple features NULL
share.y.lims Same Y-axis for all features FALSE
order Order groups by median TRUE

See also