plot_log2FC: Plot log2 fold change
In MetAlyzer: Read and Analyze 'MetIDQ™' Software Output Files

plot_log2FC

R Documentation

Plot log2 fold change

Description

This method plots the log2 fold change for each metabolite.

Usage

plot_log2FC(
  metalyzer_se,
  signif_colors = c(`#5F5F5F` = 1, `#FEBF6E` = 0.1, `#EE5C42` = 0.05, `#8B1A1A` = 0.01),
  hide_labels_for = c(),
  class_colors = "MetAlyzer",
  polarity_file = "MxPQuant500",
  vulcano = FALSE
)

Arguments

`metalyzer_se`	A Metalyzer object
`signif_colors`	signif_colors
`hide_labels_for`	vector of Metabolites or Classes for which no labels are printed
`class_colors`	class_colors
`polarity_file`	polarity_file
`vulcano`	boolean value to plot a vulcano plot

Value

ggplot object

Examples

metalyzer_se <- MetAlyzer_dataset(file_path = example_mutation_data_xl())
metalyzer_se <- filterMetabolites(
  metalyzer_se,
  drop_metabolites = "Metabolism Indicators"
)
metalyzer_se <- renameMetaData(
  metalyzer_se,
  Mutant_Control = "Sample Description"
)
metalyzer_se <- calculate_log2FC(
  metalyzer_se,
  categorical = "Mutant_Control",
  impute_perc_of_min = 0.2,
  impute_NA = TRUE
)

# p_vulcano <- plot_log2FC(metalyzer_se, vulcano=TRUE)
# p_fc <- plot_log2FC(metalyzer_se, vulcano=FALSE)

MetAlyzer documentation built on April 3, 2025, 6:32 p.m.