View source: R/pca_screeplot.R
pca_screeplot | R Documentation |
Given a PCA structure (result of the centered_pca
function), creates a screeplot of the positive eigen values
pca_screeplot(pca_struct, filepathroot=NULL)
pca_struct |
An object created by the |
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. |
A screeplot of positive eigen values
Antoine GARNIER
#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)
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