plotly_vulcano: Plotly Log2FC Vulcano Plot

In MetAlyzer: Read and Analyze 'MetIDQ™' Software Output Files

Plotly Log2FC Vulcano Plot

Description

This function returns a list with interactive vulcanoplot based on log2 fold change data.

Usage

plotly_vulcano(
  metalyzer_se,
  cutoff_y = 0.05,
  cutoff_x = 1.5,
  class_colors = metalyzer_colors()
)

Arguments

metalyzer_se	A Metalyzer object
cutoff_y	A numeric value specifying the cutoff for q-value
cutoff_x	A numeric value specifying the cutoff for log2 fold change
class_colors	A csv file containing class colors hexcodes

Value

plotly 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 <- plotly_vulcano(metalyzer_se, 
                       cutoff_y = 0.05,
                       cutoff_x = 1.5)

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