Stacked Bar Plot of Phenotype Composition

Stacked bar plot showing the proportion or count of each phenotype within each sample (or other grouping variable). Matches the stacked bar composition plots from the images.

Usage

CompositionPlot(
  object,
  group_by = "sample_id",
  proportion = TRUE,
  colours = NULL
)

Arguments

object

An SpatialCellData object with a phenotype column.

group_by

Character. Metadata column for the x-axis grouping. Default "sample_id".

proportion

Logical. Show proportions instead of counts? Default TRUE.

colours

Named character vector or NULL.

Value

A ggplot object.

Examples

counts <- matrix(rnorm(100), nrow = 50,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(50), y = runif(50))
meta <- data.frame(cell_id = 1:50,
                   sample_id = rep(c("S1", "S2"), each = 25),
                   phenotype = sample(c("T cell", "B cell", "Mac"), 50, TRUE))
obj <- CreateSpatialObject(counts, coords, meta)
CompositionPlot(obj)