# addendum to CA script by Elie Maza and Christian Chervin, AgroToulouse, to inverse axes
ellipseCA2 = function (x, ellipse = c("col", "row"), method = "multinomial", 
    nbsample = 100, axes = c(1, 2), xlim = NULL, ylim = NULL, 
    col.row = "blue", col.col = "red", col.row.ell = col.row, 
    col.col.ell = col.col, graph.type = c("ggplot", "classic"), 
    ggoptions = NULL, ...) 
{
    X <- x$call$X
    argument <- list(...)
    if (!is.null(argument[["cex"]]) & is.null(ggoptions["size"])) 
        ggoptions["size"] <- 4 * argument$cex
    ggoptions_default <- list(size = 4, point.shape = 19, line.lty = 2, 
        line.lwd = 0.5, line.color = "black", segment.lty = 1, 
        segment.lwd = 0.5, circle.lty = 1, circle.lwd = 0.5, 
        circle.color = "black", low.col.quanti = "blue", high.col.quanti = "red3")
    if (!is.null(ggoptions[1])) 
        ggoptions_default[names(ggoptions)] <- ggoptions[names(ggoptions)]
    concCol <- concRow <- X
    graph.type <- match.arg(graph.type[1], c("ggplot", "classic"))
    if (method == "multinomial") {
        proba <- unlist(c(X))
        N <- sum(proba)
        proba <- proba/N
        aa <- rmultinom(nbsample, size = N, prob = proba)
        for (i in 1:nbsample) {
            aux <- matrix(aa[, i, drop = FALSE], nrow = nrow(X))
            dimnames(aux) <- dimnames(X)
            if ("col" %in% ellipse) 
                concCol <- cbind.data.frame(concCol, aux)
            if ("row" %in% ellipse) 
                concRow <- rbind.data.frame(concRow, aux)
        }
    }
    if (method == "boot") {
        aux <- X
        ni <- apply(X, 1, sum)
        for (i in 1:nbsample) {
            for (ri in 1:nrow(X)) aux[ri, ] <- summary(cut(sample(1:ni[ri], 
                ni[ri], replace = TRUE), c(0, cumsum(t(X[ri, 
                ]))) + 0.1/ni[ri] * (0:ncol(X))), maxsum = Inf)
            if ("col" %in% ellipse) 
                concCol <- cbind.data.frame(concCol, aux)
            if ("row" %in% ellipse) 
                concRow <- rbind.data.frame(concRow, aux)
        }
    }
    if (length(col.row) == 1) 
        col.row <- rep(col.row, nrow(X))
    if (length(col.col) == 1) 
        col.col <- rep(col.col, ncol(X))
    if (length(col.col.ell) == 1) 
        col.col.ell <- rep(col.col.ell, ncol(X))
    if (length(col.row.ell) == 1) 
        col.row.ell <- rep(col.row.ell, ncol(X))
    if ("col" %in% ellipse) {
        colCA <- CA(concCol, col.sup = (ncol(X) + 1):ncol(concCol), 
            graph = FALSE)
        aux3 <- colCA$col.sup$coord[, axes]
        rownames(aux3) <- paste("r", 1:nrow(aux3), sep = "")
        aux1 <- cbind.data.frame(paste("col", 1:ncol(X), sep = ""), 
            aux3)
        aux1[, 1] <- as.factor(aux1[, 1])
        ellCol <- coord.ellipse(aux1, level.conf = 0.95)$res
    }
    if ("row" %in% ellipse) {
        rowCA <- CA(concRow, row.sup = (nrow(X) + 1):nrow(concRow), 
            graph = FALSE)
# Inversion of factorial axis 1
rowCA$row.sup$coord[,1]=-rowCA$row.sup$coord[,1]
        aux2 <- cbind.data.frame(paste("row", 1:nrow(X), sep = ""), 
            rowCA$row.sup$coord[, axes])
        aux2[, 1] <- as.factor(aux2[, 1])
        ellRow <- coord.ellipse(aux2, level.conf = 0.95)$res
    }
    nullxlimylim <- (is.null(xlim) & is.null(ylim))
    if (is.null(xlim)) {
        if (("col" %in% ellipse) & ("row" %in% ellipse)) 
            xlim <- c(min(ellCol[, 2], ellRow[, 2]), max(ellCol[, 
                2], ellRow[, 2]))
        else {
            if ("col" %in% ellipse) 
                xlim <- c(min(ellCol[, 2]), max(ellCol[, 2]))
            if ("row" %in% ellipse) 
                xlim <- c(min(ellRow[, 2]), max(ellRow[, 2]))
        }
    }
    if (is.null(ylim)) {
        if (("col" %in% ellipse) & ("row" %in% ellipse)) 
            ylim <- c(min(ellCol[, 3], ellRow[, 3]), max(ellCol[, 
                3], ellRow[, 3]))
        else {
            if ("col" %in% ellipse) 
                ylim <- c(min(ellCol[, 3]), max(ellCol[, 3]))
            if ("row" %in% ellipse) 
                ylim <- c(min(ellRow[, 3]), max(ellRow[, 3]))
        }
    }
    if (!is.null(x$row.sup)) {
        xlim <- c(min(xlim[1], min(x$row.sup$coord[, axes[1]])), 
            max(xlim[2], max(x$row.sup$coord[, axes[1]])))
        ylim <- c(min(ylim[1], min(x$row.sup$coord[, axes[2]])), 
            max(ylim[2], max(x$row.sup$coord[, axes[2]])))
    }
    if (!is.null(x$col.sup)) {
        xlim <- c(min(xlim[1], min(x$col.sup$coord[, axes[1]])), 
            max(xlim[2], max(x$col.sup$coord[, axes[1]])))
        ylim <- c(min(ylim[1], min(x$col.sup$coord[, axes[2]])), 
            max(ylim[2], max(x$col.sup$coord[, axes[2]])))
    }
    if (nullxlimylim & diff(xlim)/diff(ylim) > 3) 
        ylim <- (ylim - mean(ylim)) * diff(xlim)/diff(ylim)/3 + 
            mean(ylim)
    if (nullxlimylim & diff(xlim)/diff(ylim) < 1/2) 
        xlim <- (xlim - mean(xlim)) * diff(ylim)/diff(xlim)/2 + 
            mean(xlim)
    graph <- plot(x, axes = axes, xlim = xlim, ylim = ylim, col.col = col.col, 
        col.row = col.row, graph.type = graph.type, ggoptions = ggoptions, 
        ...)
    if ("row" %in% ellipse) {
        lev <- paste("row", 1:nlevels(ellRow[, 1]), sep = "")
        for (e in 1:nlevels(ellRow[, 1])) {
            data.elli <- ellRow[ellRow[, 1] == lev[e], -1]
            if (graph.type == "classic") {
                lines(x = data.elli[, 1], y = data.elli[, 2], 
                  col = col.row.ell[e])
            }
            if (graph.type == "ggplot") {
                graph <- graph + geom_path(aes_string(x = data.elli[, 
                  1], y = data.elli[, 2]), color = col.row.ell[e])
            }
        }
    }
    if ("col" %in% ellipse) {
        lev <- paste("col", 1:nlevels(ellCol[, 1]), sep = "")
        for (e in 1:nlevels(ellCol[, 1])) {
            data.elli <- ellCol[ellCol[, 1] == lev[e], -1]
            if (graph.type == "classic") {
                lines(x = data.elli[, 1], y = data.elli[, 2], 
                  col = col.col.ell[e])
            }
            if (graph.type == "ggplot") {
                graph <- graph + geom_path(aes_string(x = data.elli[, 
                  1], y = data.elli[, 2]), color = col.col.ell[e])
            }
        }
    }
    if (graph.type == "ggplot") 
        print(graph)
}