process_network_microbe: process_network_microbe

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

process_network_microbe

Description

Process the network from BugSigDB.

Usage

process_network_microbe(
  ret,
  delete_zero_degree = TRUE,
  make_upper = NULL,
  disease_plot = FALSE,
  ec_plot = FALSE,
  metab = NULL,
  metab_col = NULL,
  metab_thresh = 0.2,
  mb_plot = FALSE,
  ec_file = NULL,
  up_tax_file = NULL
)

Arguments

ret	biotext class object
delete_zero_degree	exclude zero degree nodes from plotting
make_upper	make these words to uppercase
disease_plot	disease plotting
ec_plot	enzyme plotting
metab	metabolite data.frame
metab_col	metabolite data frame column name in the order of "candidate taxon", "metabolite", "quantitative values for thresholding"
metab_thresh	threshold of association in metabolites - taxa relationship (e.g., correlation coefficient)
mb_plot	microbe plotting
ec_file	enzyme database file
up_tax_file	UniProt taxonomy file

Details

Perform tasks before plotting for the data from BugSigDB, like obtaining associated diseases to plot

Value

biotext class object

Examples

## Not run: 
    bugsigdb("Veillonella dispar") |> process_network_microbe()

## End(Not run)

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.