pca_2d {Bios2cor} | R Documentation |
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=NULL)
Arguments
pca_struct |
An object created by the |
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. Default is NULL (a "PCA_abs_ord.png" file will be created). 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
wd <- tempdir()
#wd <-getwd()
file <- file.path(wd,"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)
#Creating 2D plot of elements projected on default [1,2] plane
#pca_2d(pca)
[Package Bios2cor version 2.2.1 Index]