Violin Plot of Marker Expression — ViolinPlot • phenoscapR

Violin plot showing the distribution of marker expression across phenotypes or other grouping variables.

Usage

ViolinPlot(
  object,
  features,
  group_by = "phenotype",
  slot = "data",
  colours = NULL,
  ncol = NULL,
  pt_size = 0
)

Arguments

object: An SpatialCellData object.
features: Character vector. Marker names to plot.
group_by: Character. Metadata column to group by. Default "phenotype".
slot: Character. "data" or "counts".
colours: Named character vector or NULL.
ncol: Integer or NULL. Number of columns for facets.
pt_size: Numeric. Jitter point size. 0 to hide. Default 0.

Value

A ggplot object.

Examples

counts <- matrix(c(rnorm(30, 5), rnorm(30, 1)), ncol = 2,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(30), y = runif(30))
meta <- data.frame(cell_id = 1:30, sample_id = "s1",
                   phenotype = rep(c("T cell", "Other"), each = 15))
obj <- CreateSpatialObject(counts, coords, meta)
ViolinPlot(obj, features = c("CD3", "CD8"))