Plot levels of a single feature across groups

This functions takes the output from function runDE and plots the expression of a single feature across the replicates in each group for each indicated split.

Usage

plotFeature(
  input,
  feature_name,
  use_splits = NULL,
  normalization_method = "cpm",
  plot_type = "boxplot",
  title = NULL,
  subtitle = NULL,
  label_replicates = FALSE,
  label_statistics = TRUE
)

Arguments

input: Output from function runDE.
feature_name: A character string indicating which feature to plot.
use_splits: A character string or vector containing the names of splits to use. Defaults to NULL, which will try all splits.
normalization_method: A character string indicating which normalization method to apply to the replicate x feature matrix. Permitted values are "cpm", "log_cpm", and "none". Defaults to "cpm".
plot_type: A character string indicating the type of plot. Permitted values are "boxplot", "bar_se", "bar_sd", "beeswarm". Defaults to "boxplot".
title: A character string indicating the plot title. Default = NULL sets a title automatically for each split.
subtitle: Character string indicating the plot subtitle. Default = NULL automatically generates a subtitle.
label_replicates: A Boolean value indicating whether to label the replicates. Defaults to FALSE.
label_statistics: A Boolean value indicating whether to label the differential expression analysis LFC and p-value. Defaults to TRUE.

Value

If only one split is provided, a single ggplot2 object, otherwise a named list of ggplot2 objects, where each element corresponds to a split.