R/PlotProfiles.R

In maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

"PlotProfiles" <-
function (data, cond, main = NULL, cex.xaxis = 0.5, ylim = NULL, 
    repvect, sub = NULL, color.mode = "rainbow", item = NULL ) 
{
    pos.vline <- repvect[1:length(repvect)] - c(0, repvect[1:(length(repvect) - 
        1)])
    for (i in 1:length(pos.vline)) {
        if (pos.vline[i] != 0) 
            pos.vline[i] <- i
        else pos.vline[i] <- pos.vline[i - 1]
    }
    if (is.null(ylim)) {
        ylim = c(min(as.matrix(data), na.rm = TRUE) * 1.1, max(as.matrix(data), 
            na.rm = TRUE) * 1.1)
    }
    if (!is.vector(data)) {
        n = dim(data)[2]
        m = dim(data)[1]
        if (m == 1) 
            nom <- rownames(data)
        else nom <- NULL
        plot(x = c(1:n), y = data[1, ], type = "l", col = 1, 
            ylim = ylim, ylab = "expression value", xlab = " ", 
            main = paste("Cluster", main, "(",m, item, ")", 
                nom, sep=" "), xaxt = "n")
        axis(1, at = 1:n, labels = substr(cond, 1, 26), cex.axis = cex.xaxis, 
            las = 2)
        if (color.mode == "rainbow") {
            abline(v = pos.vline, col = "light gray")
            for (i in 1:dim(data)[1]) {
                lines(x = c(1:n), y = data[i, ], col = i)
            }
        }
        else if (color.mode == "gray") {
            for (i in 1:dim(data)[1]) {
                lines(x = c(1:n), y = data[i, ], col = "light gray")
            }
            yy <- apply(as.matrix(data), 2, median, na.rm = TRUE)
            lines(x = c(1:n), y = yy, col = "black")
        }
        else stop("Invalid mode, must be one of rainbow, gray")
    }
    else {
        n = length(data)
        plot(x = c(1:n), y = data, type = "l", col = 1, ylim = ylim, 
            ylab = "expression value", sub, xaxt = "n", xlab = " ")
        axis(1, at = 1:n, labels = cond, cex.axis = cex.xaxis, 
            las = 2)
        abline(v = pos.vline, col = "light gray")
    }
}