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# Bios2cor is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# See the GNU General Public License at:
# http://www.gnu.org/licenses/
#
write.pca <- function(corr_pca, filepathroot, pc= NULL, entropy= NULL){
if (missing(corr_pca)) {
stop("A PCA object created by the centered_pca function is required")
}
if (is.null(filepathroot)) {
filename <- paste(tempdir(), "/PCA_COORD.csv", sep="")
}else{
filename <-paste(filepathroot, "_PCA_COORD.csv", sep="")
}
pca_coord <- corr_pca$coord
pca_positions <- rownames(pca_coord)
pca_size <- length(pca_coord[,1])
if (is.null(pc)) {
pca_dim <- length(pca_coord[1,])
} else {
pca_dim <- pc
}
head <- "position"
if(!is.null(entropy)) {
head <- paste(head, "entropy")
}
lapply(1:pca_dim, function(dim){
head <<- paste(head, paste("PCA", dim, sep= ""))
})
write(head, file= filename, append= FALSE)
if(!is.null(entropy)) {
for(pos in 1:pca_size){
pos_line <- pca_coord[pos,]
position <- pca_positions[pos]
entropy_val <- format(as.numeric(entropy[position]), digits=3, nsmall=3)
#Ignoring possible NaN values
if(sum(is.na(pos_line)) <= 0){
coord_tmp <- paste(pca_coord[pos, 1:pca_dim], collapse= " ")
current_line <- paste(position, entropy_val, coord_tmp)
write(current_line, file= filename, append= TRUE)
}
}
} else {
for(pos in 1:pca_size){
pos_line <- pca_coord[pos,]
position <- pca_positions[pos]
#Ignoring possible NaN values
if(sum(is.na(pos_line)) <= 0){
coords <- ""
for(dim in 1:pca_dim){
coords <- paste(coords, pca_coord[pos,dim])
}
current_line <- paste(position, coords, sep= "")
write(current_line, file= filename, append= TRUE)
}
}
}
}
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