Pipe_analysis

1. Analysis options setup

## View current global analysis options
getOption("LorMe")

## Set analysis options
LorMe_options(
  global = list(Analysis_level = "Genus"),
  sub_net = list(threshold = 0.7),
  all_net = list(threshold = 0.7)
)

2. One-line analysis

Two_group_analysis <- LorMe_pipeline(Two_group)

notes: ‘step’ can be used for specifying analysis modules to run.

3. Results extraction

## Access results:
# Alpha diversity
Two_group_analysis$alpha_results$plotlist$Plotobj_Shannon$Boxplot

# Beta diversity
Two_group_analysis$beta_results$PCoA_Plot

# Community composition
Two_group_analysis$composition_results$barplot

# Differential analysis
Two_group_analysis$Deseq_volcano$FC_FDR

Two_group_analysis$Deseq_manhattan$manhattan

# Differential barplot
library(patchwork)
Two_group_analysis$diffbar_result$Barplot |
  Two_group_analysis$diffbar_result$Differenceplot

# Subnetworks
require(magrittr)

## 载入需要的程序包：magrittr

Two_group_analysis$sub_network_results$Treatment_sub_network %>%
  network_visual()

# Combined network
Two_group_analysis$combine_network_results %>% network_visual()

## Reset to default options
LorMe_defaults()

Go Step-by-Step Analysis