pca_2d: PCA projection on two dimensions

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

PCA projection on two dimensions

Description

Given an object of class 'pca' (result of the centered_pca function), draws a graph of the projection of the elements on two dimensions (first and second components by default)

Usage

  pca_2d(pca_struct, abs= 1, ord= 2, filepathroot)

Arguments

pca_struct	An object created by the centered_pca function
abs	An integer which corresponds to the x axis of the projection plane. Default is 1 (first component)
ord	An integer which corresponds to the y axis of the projection plane. Default is 2 (second component)
filepathroot	The root of the full path name for the output file. If NULL, a "PCA_abs_ord.png" file will be created in tempdir(). If not NULL, the filepathroot will have the "_PCA_abs_ord.png" extension.

Value

A 2D graph of the projection of the elements on selected two principal components

Author(s)

Antoine GARNIER

Examples

  #File path for output files
  out <- tempdir()
  file <- file.path(out,"test_seq2") 

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

  #Creating OMES correlation object
  omes <- omes(align, gap_ratio = 0.2)

  #Creating entropy object
  #entropy <- entropy(align)

  #Selecting correlation matrix
  omes <-omes$Zscore

  #Creating PCA object for selected correlation matrix and saving eigen values
  pca <- centered_pca(omes, filepathroot= file, pc= NULL, dec_val= 5, filter= NULL)

  #Creating 2D plot of elements projected on selected [abs,ord] plane 
  pca_2d(pca, abs = 1, ord = 3, file)
 

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