pca_screeplot {Bios2cor}

Creates PCA screeplot

Description

Given a PCA structure (result of the centered_pca function), creates a screeplot of the positive eigen values

Usage

  pca_screeplot(pca_struct, filepathroot=NULL)

Arguments

pca_struct

An object created by the centered_pca function

filepathroot

The root of the full path name for the output file. Default is NULL (a "EIGEN.png" file will be created). If not NULL, the filepathroot will have the "_EIGEN.png" extension.

Value

A screeplot of positive eigen values

Author(s)

Antoine GARNIER

Examples

  #File path for output files
  wd <- tempdir()
  #wd <-getwd() 
  file <- file.path(wd,"test_seq3") 

  #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)

  #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)

  #Plotting scree plot 
  pca_screeplot(pca, file)
  #pca_screeplot(pca)