plot_distribution: Plot distribution of expression values for each sample

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

Plot distribution of expression values for each sample

Description

Use boxplots, violin plots or quantile plots (in form of parallel coordinate plots of the quantiles) to compare the distribution of expression values for each sample.

Usage

plot_distribution(
  se,
  assay = 1,
  method = "quantileplot",
  coef = 5,
  label = "expression value",
  title = paste("Distribution of expression", "values in each sample")
)

Arguments

se	RangedSummarizedExperiment-class object
assay	Character or integer. Name or number of assay to be used for plotting.
method	Method to use for plotting: "quantileplot" (default), "boxplot", "violinplot".
coef	Numeric. Used in outlier definition (median +/- coef * IQR)
label	Character. Label of x or y axis (default: "expression value").
title	Character. Title of the plot.

Value

List with the following components:

• info: data.frame with information about outlier samples or NULL

• plot: plot as returned by ggparcoord (quantile plot), ggplot (boxplot) or ggviolin (violin plot)

Examples

data("se.gene")

## quantile plot
plot_distribution(se = se.gene,
                  method = "quantileplot")

## boxplot
plot_distribution(se = se.gene,
                  method = "boxplot")

## violinplot
library("ggpubr")
plot_distribution(se = se.gene,
                  method = "violinplot")

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.