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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/
#
pca_screeplot <- function(pca_struct, filepathroot){
pca_coord <- pca_struct$coord
nb_component <- length(pca_coord[1,])
pca_positions <- rownames(pca_coord)
components <- 1:nb_component
variances <- unlist(lapply(1:nb_component, function(x){var(pca_coord[,x])}))
if(is.null(filepathroot)) {
filename <- paste(tempdir(), "/SCREEPLOT.png", sep="")
} else {
filename <- paste(filepathroot, "_SCREEPLOT.png", sep="")
}
png(filename, width = 600, height = 600, units = "px")
plot(components, variances, main= basename(filename))
lines(components, variances)
dev.off()
}
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