R/weightsplot.R

In mvdalab: Multivariate Data Analysis Laboratory

weightsplot <- function(object, ncomp = object$ncomp, conf = .95, verbose = FALSE) {
  if (object$val.method == "none" | object$val.method == "loo") {
    if(length(ncomp) == 1) {
      ncomp <- ncomp
      Stack <- data.frame(object$weights[, ncomp])
      names(Stack) <- ncomp
      df <- reshape(Stack, idvar = "variable", varying = list(1),
                      times = names(Stack[1]),
                      v.names = "value", direction = "long",
                      ids = row.names(Stack))
      row.names(df) <- NULL
      names(df)[1] <- "ncomp"
    } else {
      ncomp <- ncomp
      Stack <- data.frame(object$weights[, ncomp])
      names(Stack) <- ncomp
      Stack$variable <- row.names(Stack)
      df <- melt(Stack, measure = 1:length(ncomp))
      names(df)[2] <- "ncomp"
    }
    print(with(df, ggplot(df, aes(reorder(variable, -abs(value), mean), value)) +
            theme_bw() +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
            geom_point(size = 3) +
            geom_hline(yintercept = 0) +
            ylab("Weights") +
            xlab("Variables") +
            theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
            ggtitle("Weights Plot") +
            facet_wrap(~ncomp, scales = "free_y") +
            theme(strip.text.x = element_text(size = 10, face = "bold")) +
            xlab("Variables") +
            theme(legend.position = "none") +
            theme(plot.title = element_text(size = 20)) +
            theme(axis.title.x = element_text(size = 15)) +
            theme(axis.title.y = element_text(size = 15, angle = 90)) +
            theme(axis.text.x = element_text(size = 10, angle = 90, vjust = 0.5, face = "bold")) +
            theme(axis.text.y = element_text(size = 10, angle = 0, face = "bold"))))
  } else {
    A <- do.call("rbind", weights.mvdareg(object, ncomp, conf = conf))
    df <- melt(A[, c(1, 6, 4:5, 2)], measure = 3:4, variable.name = "CI")
    df <- subset(df, ncomp = ncomp)
    print(with(df, ggplot(df, aes(reorder(variable, -abs(value), mean), value)) +
            theme_bw() +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
            geom_line() +
            geom_hline(yintercept = 0) +
            ylab("Weights") +
            xlab("Variables") +
            theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
            ggtitle("Weights Plot") +
            facet_wrap(~ncomp, scales = "free_y") +
            theme(strip.text.x = element_text(size = 10, face = "bold")) +
            theme(legend.position = "none") +
            theme(plot.title = element_text(size = 20)) +
            theme(axis.title.x = element_text(size = 15)) +
            theme(axis.title.y = element_text(size = 15, angle = 90)) +
            theme(axis.text.x = element_text(size = 10, angle = 90, vjust = 0.5, face = "bold")) +
            theme(axis.text.y = element_text(size = 10, angle = 0, face = "bold"))))
    if(verbose == TRUE) {
      return(A)
    }
  }
}