plotly_network: Plotly Log2FC Network Plot

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

Plotly Log2FC Network Plot

Description

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

Usage

plotly_network(
  metalyzer_se,
  q_value = 0.05,
  metabolite_node_size = 11,
  connection_width = 1.25,
  pathway_text_size = 20,
  pathway_width = 10,
  plot_height = 800
)

Arguments

metalyzer_se	A MetAlyzer Object
q_value	A numeric value specifying the cutoff for q-value
metabolite_node_size	The text size of the metabolite Nodes
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
plot_height	The height of the Plot in pixel [px]

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 = FALSE
)

p_network <- plotly_network(metalyzer_se, q_value = 0.05)

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