Ridge Plot of Marker Expression

Ridge (joy) plot showing the distribution of marker expression for each group. Implemented with overlapping density plots.

Usage

RidgePlot(
  object,
  features,
  group_by = "phenotype",
  slot = "data",
  colours = NULL,
  ncol = NULL
)

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.

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)
RidgePlot(obj, features = "CD3")