plot_network {MetAlyzer}

Plot Pathway Network

Description

This function plots the log2 fold change for each metabolite and visualizes it, in a pathway network.

Usage

plot_network(
  metalyzer_se,
  q_value = 0.05,
  metabolite_text_size = 3,
  connection_width = 0.75,
  pathway_text_size = 6,
  pathway_width = 4,
  scale_colors = c("green", "black", "magenta")
)

Arguments

metalyzer_se

A Metalyzer object

q_value

The q-value threshold for significance

metabolite_text_size

The text size of metabolite labels

connection_width

The line width of connections between metabolites

pathway_text_size

The text size of pathway annotations

pathway_width

The line width of pathway-specific connection coloring

scale_colors

A vector of length 3 with colors for low, mid and high of the gradient.

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 = FALSE
)

network <- plot_network(metalyzer_se, q_value = 0.05)