network.plot: Creates network structure of top elements

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Creates network structure of top elements

Description

Given a top_pairs object (result of the top_pairs_analysis function), creates a network to visualize the elements involved in the top scoring pairs and their links

Usage

  network.plot(top_pairs, filepathroot)

Arguments

top_pairs	An object of class 'top_pairs' created by the top_pairs_analysis function
filepathroot	The root of the full path name for the output file. If NULL, a "NETWORK.pdf" file will be created in tempdir(). If not NULL, the filepathroot will have the "_NETWORK.pdf" extension.

Value

A network representing links between elements in the top scoring pairs

Author(s)

Antoine GARNIER

Examples

  #File path for output file
  out <- tempdir()
  file <- file.path(out,"test_omes") 

  #Importing MSA file
  msf <- system.file("msa/toy_align.msf", package = "Bios2cor")
  align <- import.msf(msf)

  #Creating OMES correlation object for positions with gap ratio < 0.2
  omes <- omes(align, gap_ratio= 0.2)
  
  #Selecting a correlation matrix
  omes <-omes$Zscore
   
  #Analyzing pairs with top scores and creating 'top_pairs' object
  top_pairs <- top_pairs_analysis(omes, top = 25, file)

  #Plotting the network structure of top pairs in pdf file 
  network.plot(top_pairs, file)

Bios2cor documentation built on April 4, 2025, 4:14 a.m.