R/IsoPlotVec2.R

In IsoGeneGUI: A graphical user interface to conduct a dose-response analysis of microarray data

IsoPlotVec2 <- function (x, y, type = c("continuous", "ordinal"), add.curve = FALSE) 
{
    y<-as.numeric(y)
    type <- match.arg(type)
    if (!(type %in% c("continuous", "ordinal"))) 
        stop("The dose can be only continuous or ordinal")
    miny <- min(y)
    maxy <- max(y)
    ordx <- order(x)
    unx <- sort(unique(x))
    y1 <- as.numeric(y)[ordx]
    y.m <- tapply(y1, as.factor(x[order(x)]), mean)
    y.m.tot <- rep(mean(y), length(unx))
    n.p <- table(x)
    n.g <- length(n.p)
    y.is.u <- pava(y.m, w = n.p)
  #  y.is.d <- rev(pava(rev(y.m), w = rev(n.p)))
    y.is.d <- pava(y = y.m, w = n.p, decreasing=TRUE)  
    
    
    dire <- IsoGene1(x, as.numeric(y))[[11]]
    if (type == "continuous") {
        plot(sort(x), y1, lwd = 2, xlab = "Doses", ylab = "Response")
        points(sort(unique(x)), y.m, pch = "+", lwd = 3, col = 2)
        if (dire == "u") {
            points(unx, y.is.u, pch = "*", lwd = 2)
            if (add.curve) 
                lines(unx, y.is.u, lty = 1, col = 4, lwd = 2)
        }
        else {
            points(unx, y.is.d, pch = "*", lwd = 2)
            if (add.curve) 
                lines(unx, y.is.d, lty = 1, col = 4, lwd = 2)
        }
    }
    else {
        catx <- factor(x, levels = sort(unique.default(x)), labels = unx, 
            ordered = FALSE)
        a <- 1:length(unx)
        plot(a, ylim = c(miny, maxy), pch = "", ylab = "Response", 
            xlab = "Doses", axes = FALSE,frame.plot=T)
        axis(1, sort(unique(a)), as.character(unx))
        axis(2)
        points(catx, y, lwd = 2)
        points(sort(unique(catx)), y.m, pch = "+", lwd = 3, col = 2)
        if (dire == "u") {
            points(a, y.is.u, pch = "*", lwd = 2)
            if (add.curve) 
                lines(a, y.is.u, lty = 1, col = 4, lwd = 2)
        }
        else {
            points(a, y.is.d, pch = "*", lwd = 2)
            if (add.curve) 
                lines(a, y.is.d, lty = 1, col = 4, lwd = 2)
        }
    }
    title(paste("Sample: ", row.names(y), sep = ""))
}