plot_density: Density plot of expression values

In jcalendo/coriell: Convenience Functions for Bioinformatics

Density plot of expression values

Description

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)

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

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.