Module_abundance: Calculate network module abundance for each sample

In LorMe: Lightweight One-Line Resolving Microbial Ecology Program

Calculate network module abundance for each sample

Description

Calculate network module abundance for each sample

Usage

Module_abundance(network_obj, No.module)

Arguments

network_obj	Network analysis results generated from network_analysis
No.module	Numeric or numeric vector of No.module

Value

A list containing module abundance in metafile and column table of corresponding data frame

Examples

# data preparation
data("Two_group")
## network analysis
network_results <- network_analysis(taxobj = Two_group,
                                    taxlevel = "Genus",
                                    n = 10,
                                    threshold = 0.8)
require(ggplot2)
# one module
moduleframe <- Module_abundance(network_obj = network_results, No.module = 3)
moduleframe$rowframe        # combine into metafile
moduleframe$columnframe     # column table
# statistics
moduleframe$plotlist$Plotobj_Module3$Statistics
# extract plot
moduleframe$plotlist$Plotobj_Module3$Barplot
moduleframe$plotlist$Plotobj_Module3$Boxplot
moduleframe$plotlist$Plotobj_Module3$Violinplot

# multiple modules
moduleframe <- Module_abundance(network_results, c(1, 3, 6))
moduleframe$rowframe
moduleframe$columnframe # column table can be used in ggplot visualization
# same as above to extract plots and statistics
moduleframe$plotlist$Plotobj_Module6$Barplot

LorMe documentation built on Jan. 12, 2026, 9:06 a.m.