plot_boxplot: Create boxplot from expression data

In jcalendo/coriell: Convenience Functions for Bioinformatics

Create boxplot from expression data

Description

Create a boxplot (or violin plot) of expression distributions for the given expression matrix. Optionally plot the relative log expression of the matrix.

Usage

plot_boxplot(x, ...)

## Default S3 method:
plot_boxplot(x)

## S3 method for class 'matrix'
plot_boxplot(
  x,
  metadata = NULL,
  fillBy = NULL,
  rle = FALSE,
  violin = FALSE,
  ...
)

## S3 method for class 'data.frame'
plot_boxplot(
  x,
  metadata = NULL,
  fillBy = NULL,
  rle = FALSE,
  violin = FALSE,
  ...
)

## S3 method for class 'SummarizedExperiment'
plot_boxplot(
  x,
  assay = "counts",
  fillBy = NULL,
  rle = FALSE,
  violin = FALSE,
  ...
)

Arguments

x	matrix of expression values or SummarizedExperiment object
...	Additional parameters passed to ggplot2::geom_boxplot() or ggplot2::geom_violin()
metadata	data.frame containing metadata per sample. rownames of metadata must match the colnames of the input matrix. Default NULL, each sample in x will be plotted individually.
fillBy	metadata column used to fill boxplots. Default NULL, each sample will be a distinct color.
rle	Plot the relative log expression value. This option assumes that the input matrix has already been logged. Be sure to take the log of the input matrix prior to setting this option.
violin	Plot the data as a violin plot instead of a boxplot. Default FALSE.
assay	If a SummarizedExperiment is supplied what assay is used. 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 boxplot by sample
plot_boxplot(GSE161650_lc)
 
# Plot the boxplot by coloring each Group
plot_boxplot(GSE161650_lc, metadata, fillBy = "Group") 

# Create a violin plot after RLE transformation
plot_boxplot(GSE161650_lc, metadata, fillBy = "Group", rle = TRUE, violin = TRUE)

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