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#' @title Plot method for an object of class \code{ortho_projection}
#' @description
#' Plots objects of class \code{ortho_projection}
#' @aliases plot.ortho_projection
#' @usage \method{plot}{ortho_projection}(x, col = "dodgerblue", ...)
#' @param x an object of class \code{ortho_projection} (as returned by \code{ortho_projection}).
#' @param col the color of the plots (default is "dodgerblue")
#' @param ... arguments to be passed to methods.
#' @author Leonardo Ramirez-Lopez and Antoine Stevens
#' @seealso \code{\link{ortho_projection}}
#' @importFrom graphics barplot
#' @export
plot.ortho_projection <- function(x, col = "dodgerblue", ...) {
x_variance <- x$variance$x_var
if (x$pc_selection$method == "opc") {
tpl <- x$opc_evaluation[, c(1, ncol(x$opc_evaluation))]
if ("mean_standardized_rmsd_Yr" %in% colnames(tpl)) {
ylab <- "mean of the standardized RMSD of all Y variables"
}
if (colnames(tpl)[2] %in% c("rmsd_Yr", "rmsd")) {
ylab <- "RMSD of Yr"
}
if (colnames(tpl)[2] == "kappa") {
ylab <- "kappa index"
}
plot(tpl,
type = "p",
ylab = ylab, pch = 1, col = col, ...
)
grid()
segments(tpl[, 1], 0, tpl[, 1], tpl[, 2], col = col)
} else {
opar <- par("mfrow")
on.exit(par(opar))
o_mfrow <- par()$mfrow
par(mfrow = c(1, 2))
barplot(x_variance[grep("^explained_var", rownames(x_variance)), ],
horiz = F,
names.arg = colnames(x_variance), ylim = c(0, 1),
ylab = "Explained variance", col = col, ...
)
barplot(x_variance[grep("cumulative", rownames(x_variance)), ],
horiz = F,
names.arg = colnames(x_variance), ylim = c(0, 1),
ylab = "Explained variance (cumulative)", col = col, ...
)
}
}
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