Module_abundance: Calculate network module abundance for each sample

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

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 Sept. 13, 2024, 9:07 a.m.