Density plot of expression values — plot

Create a density plot of expression values for the given expression matrix.

Usage

plot_density(x, ...)

# Default S3 method
plot_density(x)

# S3 method for class 'matrix'
plot_density(x, metadata = NULL, colBy = NULL, ...)

# S3 method for class 'data.frame'
plot_density(x, metadata = NULL, colBy = NULL, ...)

# S3 method for class 'SummarizedExperiment'
plot_density(x, assay = "counts", colBy = NULL, ...)

Arguments

x: gene by sample matrix or SummarizedExperiment object
...: Additional parameters passed to ggplot2::geom_density()
metadata: data.frame containing metadata per sample. rownames of metadata must match the colnames of the input matrix. Default NULL, each sample in the matrix will be plotted.
colBy: metadata column used to color density lines. Default NULL, each sample in the matrix will be plotted.
assay: assay of the SummarizedExperiment object. Default "counts"

Value

ggplot object

Examples

# Create metadata for plotting
metadata <- data.frame(row.names = colnames(GSE161650_lc))
metadata$Group <- rep(c("DMSO", "THZ1"), each = 3)

# Plot the density by sample
plot_density(GSE161650_lc) +
  theme_coriell()


# Color each sample by their Group in metadata
plot_density(GSE161650_lc, metadata, colBy = "Group") +
  theme_coriell()