R/plot.fast.R

In SensoMineR: Sensory data analysis with R

plot.fast=function (x,choix="ind", axes = c(1, 2), xlim = NULL, ylim = NULL, invisible = NULL,
    col.ind = "blue", col.var = "red", col.quali.sup = "darkred",
    col.ind.sup = "darkblue", col.quanti.sup = "black", label = "all",
    cex = 1,lab.grpe = TRUE, title = NULL, habillage = "none", palette = NULL,
    new.plot = TRUE, ...)
{
    res.mca <- x
    if (!inherits(res.mca, "catego"))
        stop("non convenient data")
    if (is.null(palette))
        palette(c("black", "red", "green3", "blue", "cyan", "magenta",
            "darkgray", "darkgoldenrod", "darkgreen", "violet",
            "turquoise", "orange", "lightpink", "lavender", "yellow",
            "lightgreen", "lightgrey", "lightblue", "darkkhaki",
            "darkmagenta", "darkolivegreen", "lightcyan", "darkorange",
            "darkorchid", "darkred", "darksalmon", "darkseagreen",
            "darkslateblue", "darkslategray", "darkslategrey",
            "darkturquoise", "darkviolet", "lightgray", "lightsalmon",
            "lightyellow", "maroon"))
    lab.ind <- lab.var <- lab.quali.sup <- lab.ind.sup <- FALSE
    if (length(label) == 1 && label == "all")
        lab.ind <- lab.var <- lab.quali.sup <- lab.ind.sup <- TRUE
    if ("ind" %in% label)
        lab.ind <- TRUE
    if ("var" %in% label)
        lab.var <- TRUE
#    if ("quali.sup" %in% label)
#        lab.quali.sup <- TRUE
#    if ("ind.sup" %in% label)
#        lab.ind.sup <- TRUE
    test.invisible <- vector(length = 5)
    if (!is.null(invisible)) {
        test.invisible[1] <- match("ind", invisible)
        test.invisible[2] <- match("var", invisible)
      #  test.invisible[3] <- match("quanti.sup", invisible)
#        test.invisible[4] <- match("ind.sup", invisible)
#        test.invisible[5] <- match("quali.sup", invisible)
    }
    else test.invisible <- rep(NA, 5)
    coord.var <- res.mca$var$coord[, axes]
    coord.ind <- res.mca$ind$coord[, axes]
#    coord.ind.sup <- coord.quali.sup <- NULL
#    if (!is.null(res.mca$ind.sup))
#        coord.ind.sup <- res.mca$ind.sup$coord[, axes]
#    if (!is.null(res.mca$quali.sup))
#        coord.quali.sup <- res.mca$quali.sup$coord[, axes]
    if (is.null(xlim)) {
        xmin <- xmax <- 0
        if (is.na(test.invisible[1]))
            xmin <- min(xmin, coord.ind[, 1])
        if (is.na(test.invisible[1]))
            xmax <- max(xmax, coord.ind[, 1])
        #if (is.na(test.invisible[4]))
#            xmin <- min(xmin, coord.ind.sup[, 1])
#        if (is.na(test.invisible[4]))
#            xmax <- max(xmax, coord.ind.sup[, 1])
        if (is.na(test.invisible[2]))
            xmin <- min(xmin, coord.var[, 1])
        if (is.na(test.invisible[2]))
            xmax <- max(xmax, coord.var[, 1])
      #  if (is.na(test.invisible[5]))
#            xmin <- min(xmin, coord.quali.sup[, 1])
#        if (is.na(test.invisible[5]))
#            xmax <- max(xmax, coord.quali.sup[, 1])
        xlim <- c(xmin, xmax) * 1.2
    }
    else {
        xmin = xlim[1]
        xmax = xlim[2]
    }
    if (is.null(ylim)) {
        ymin <- ymax <- 0
        if (is.na(test.invisible[1]))
            ymin <- min(ymin, coord.ind[, 2])
        if (is.na(test.invisible[1]))
            ymax <- max(ymax, coord.ind[, 2])
        #if (is.na(test.invisible[4]))
#            ymin <- min(ymin, coord.ind.sup[, 2])
#        if (is.na(test.invisible[4]))
#            ymax <- max(ymax, coord.ind.sup[, 2])
        if (is.na(test.invisible[2]))
            ymin <- min(ymin, coord.var[, 2])
        if (is.na(test.invisible[2]))
            ymax <- max(ymax, coord.var[, 2])
        #if (is.na(test.invisible[5]))
#            ymin <- min(ymin, coord.quali.sup[, 2])
#        if (is.na(test.invisible[5]))
#            ymax <- max(ymax, coord.quali.sup[, 2])
        ylim <- c(ymin, ymax) * 1.2
    }
    else {
        ymin = ylim[1]
        ymax = ylim[2]
    }
    if (habillage == "quali") {
        aux = 1
        col.var = NULL
        for (j in res.mca$call$quali) {
            col.var <- c(col.var, rep(aux, nlevels(res.mca$call$X[,
                j])))
            aux = aux + 1
        }
        #if (!is.null(res.mca$call$quali.sup)) {
#            col.quali.sup = NULL
#            for (j in res.mca$call$quali.sup) {
#                col.quali.sup <- c(col.quali.sup, rep(aux, nlevels(res.mca$call$X[,
#                  j])))
#                aux = aux + 1
#            }
#        }
    }
    if ((habillage != "none") & (habillage != "quali")) {
        if (!is.factor(res.mca$call$X[, habillage]))
            stop("The variable ", habillage, " is not qualitative")
        col.ind <- as.numeric(as.factor(res.mca$call$X[, habillage]))
        n.mod <- nlevels(as.factor(res.mca$call$X[, habillage]))
      #  col.ind.sup <- col.ind[res.mca$call$ind.sup]
        #if (!is.null(res.mca$call$ind.sup))
#            col.ind <- col.ind[-res.mca$call$ind.sup]
    }
    if (choix=="ind" | choix=="var"){
    sub.titre <- NULL
    titre = title
    if (is.null(title))
        titre <- "SortingTask factor map"
    else sub.titre <- "SortingTask factor map"
    if (is.na(test.invisible[1]) | is.na(test.invisible[2]) |
        is.na(test.invisible[4]) | is.na(test.invisible[5])) {
        if (new.plot) dev.new()
        plot(0, 0, main = titre, xlab = paste("Dim ", axes[1],
            " (", signif(res.mca$eig[axes[1], 2], 4), "%)", sep = ""),
            ylab = paste("Dim ", axes[2], " (", signif(res.mca$eig[axes[2],
                2], 4), "%)", sep = ""), xlim = xlim, ylim = ylim,
            col = "white", asp = 1, cex = cex)
        if (!is.null(sub.titre))
            title(sub = sub.titre, cex.sub = cex, font.sub = 2,
                col.sub = "steelblue4", adj = 0, line = 3.8)
        abline(v = 0, lty = 2, cex = cex)
        abline(h = 0, lty = 2, cex = cex)
        if (is.na(test.invisible[1])) {
            points(coord.ind, pch = 16, col = col.ind)
            if (lab.ind)
                text(coord.ind[, 1], y = coord.ind[, 2], labels = rownames(coord.ind),
                  pos = 3, col = col.ind, cex = cex)
        }
        if (is.na(test.invisible[2])) {
            points(coord.var[, 1], y = coord.var[, 2], pch = 17,
                col = col.var, cex = cex)
            if (lab.var)
                text(coord.var[, 1], y = coord.var[, 2], labels = rownames(coord.var),
                  pos = 3, col = col.var, cex = cex)

        #if (!is.null(res.mca$quali.sup) & is.na(test.invisible[5])) {
#            points(coord.quali.sup[, 1], y = coord.quali.sup[,
#                2], pch = 17, col = col.quali.sup, cex = cex)
#            if (lab.quali.sup)
#                text(coord.quali.sup[, 1], y = coord.quali.sup[,
#                  2], labels = rownames(coord.quali.sup), pos = 3,
#                  col = col.quali.sup, cex = cex)
#        }
        #if (!is.null(res.mca$ind.sup) & is.na(test.invisible[4])) {
#            points(coord.ind.sup[, 1], y = coord.ind.sup[, 2],
#                pch = 16, col = col.ind.sup, cex = cex)
#            if (lab.ind.sup)
#                text(coord.ind.sup[, 1], y = coord.ind.sup[,
#                  2], labels = rownames(coord.ind.sup), pos = 3,
#                  col = col.ind.sup, cex = cex)
#        }
        if ((habillage != "none") & (habillage != "quali") &
            (is.na(test.invisible[1]) | is.na(test.invisible[2])))
            legend("topleft", legend = levels(res.mca$call$X[,
                habillage]), text.col = 1:n.mod, cex = 0.8)
    }
    }
    }
#    if (!is.null(res.mca$quanti.sup) & is.na(test.invisible[3])) {
#        if (new.plot)
#            get(getOption("device"))(width = 8, height = 8)
#        plot(0, 0, main = "Supplementary variables on the MCA factor map",
#            xlab = paste("Dim ", axes[1], " (", signif(res.mca$eig[axes[1],
#                2], 4), "%)", sep = ""), ylab = paste("Dim ",
#                axes[2], " (", signif(res.mca$eig[axes[2], 2],
#                  4), "%)", sep = ""), xlim = c(-1.1, 1.1), ylim = c(-1.1,
#                1.1), col = "white", asp = 1, cex = cex)
#        abline(v = 0, lty = 2, cex = cex)
#        abline(h = 0, lty = 2, cex = cex)
#        x.cercle <- seq(-1, 1, by = 0.01)
#        y.cercle <- sqrt(1 - x.cercle^2)
#        lines(x.cercle, y = y.cercle)
#        lines(x.cercle, y = -y.cercle)
#        for (v in 1:nrow(res.mca$quanti.sup$coord)) {
#            arrows(0, 0, res.mca$quanti.sup$coord[v, 1], res.mca$quanti.sup$coord[v,
#                2], length = 0.1, angle = 15, code = 2, col = col.quanti.sup)
#            if (abs(res.mca$quanti.sup$coord[v, 1]) > abs(res.mca$quanti.sup$coord[v,
#                2])) {
#                if (res.mca$quanti.sup$coord[v, 1] >= 0)
#                  pos <- 4
#                else pos <- 2
#            }
#            else {
#                if (res.mca$quanti.sup$coord[v, 2] >= 0)
#                  pos <- 3
#                else pos <- 1
#            }
#            text(res.mca$quanti.sup$coord[v, 1], y = res.mca$quanti.sup$coord[v,
#                2], labels = rownames(res.mca$quanti.sup$coord)[v],
#                pos = pos, cex = cex, col = col.quanti.sup)
#        }
#    }
group=nrow(res.mca$group$coord)
    if (choix == "group") {
        if (new.plot)
            dev.new()
        if (is.null(title))
            title <- "Consumers representation"
        else sub.title <- "Consumers representation"
        coord.actif <- res.mca$group$coord[, axes]
        #if (!is.null(res.mca$group$coord.sup))
#            coord.illu <- res.mca$group$coord.sup[, axes]
#        if (is.null(col.hab)) {
#            col.hab = rep("darkred", nrow(coord.actif))
            #if (!is.null(res.mca$group$coord.sup))
#                col.hab = c(col.hab, rep("darkolivegreen", nrow(coord.illu)))
#        }
     #   if (habillage == "group")
#            col.hab <- (2:(length(group) + 1))
        plot(coord.actif, xlab = paste("Dim ", axes[1], " (", signif(res.mca$eig[axes[1],
                2], 4), "%)", sep = ""), ylab = paste("Dim ", axes[2], " (", signif(res.mca$eig[axes[2],
                2], 4), "%)", sep = ""), xlim = c(0,
            1), ylim = c(0, 1), pch = 17,
            cex = cex, main = title, cex.main = cex * 1.2, asp = 1)
        title(cex.sub = cex, font.sub = 2, col.sub = "steelblue4",
            adj = 0, line = 3.8)
         if (lab.grpe)
            text(coord.actif[, 1], y = coord.actif[, 2], labels = rownames(coord.actif),
                pos = 3)
        #if (!is.null(res.mca$group$coord.sup)) {
#            points(coord.illu, pch = 17, col = col.hab[(nrow(coord.actif) +
#                1):(nrow(coord.actif) + nrow(coord.illu))])
#            if (lab.grpe)
#                text(coord.illu[, 1], y = coord.illu[, 2], labels = rownames(coord.illu),
#                  pos = 3, col = col.hab[(nrow(coord.actif) +
#                    1):(nrow(coord.actif) + nrow(coord.illu))])
#        }
#    }
}
}