Plot marker density across images — plot_marker

Generates a density plot for a single marker using the specified assay, with curves colored by the image/sample column. Useful for quick QC of normalisation steps.

Usage

plot_marker_density(
  spe,
  marker,
  assay_name = "exprs",
  image_col = "image_name",
  title = NULL,
  show_legend = FALSE
)

Arguments

spe: A `SpatialExperiment`/`SingleCellExperiment` with the target assay and metadata in `colData()`.
marker: Marker name to plot (must match a row in the assay).
assay_name: Assay name to pull values from. Default "exprs".
image_col: Column in `colData()` used to color densities. Default "image_name".
title: Optional plot title. Defaults to "Density of {marker} (assay: {assay_name})".
show_legend: Logical; whether to show the legend. Default `FALSE`.

Value

A `ggplot` object.

Examples

data("cytoGateR_example", package = "cytoGateR")
spe <- cytoGateR_example
plot_marker_density(
  spe,
  marker = rownames(spe)[1],
  image_col = "image_name"
)