R/dualplot.R

In ctlab/ClusDec: Clustering approach to solve complete Deconvolution problem

# dualplot

dualplot <- function(x1, y1, y2, x2 = x1,
                     col = c("#C54E6D", "#009380"),
                     lwd = c(1, 1), colgrid = NULL,
                     mar = c(3, 6, 3, 6) + 0.1,
                     ylab1 = paste(substitute(y1), collapse = ""),
                     ylab2 = paste(substitute(y2), collapse = ""),
                     nxbreaks = 5,
                     yleg1 = paste(gsub("\n$", "", ylab1), "(left axis)"),
                     yleg2 = paste(ylab2, "(right axis)"),
                     ylim1 = NULL, ylim2 = NULL, ylim.ref = NULL,
                     xlab = "", main = NULL, legx = "topleft", legy = NULL,
                     silent = FALSE, bty = "n", ...){
    # Base graphics function for drawing dual axis line plot.
    # Assumed to be two time series on a conceptually similar, non-identical scale
    #
    # Assumes data is in sequence of x1 and of x2 ie ordered by time
    #
    # Use with caution!
    # Please don't use to show growth rates and the original
    # series at the same time!
    #
    # Peter Ellis, 16-27 August 2016, GNU GPL-3
    # most parameters should be obvious:
    # x1 and y1 are the x and y coordinates for first line
    # x2 and y2 are the x and y coordinates for second line.  Often x2 will == x1, but can be overridden
    # ylim1 and ylim2 are the vertical limits of the 2 axes.  Recommended NOT to use these, as
    #    the default algorithm will set them in a way that makes the axes equivalent to using an index (for
    #    positive data) or mean of each series +/- 3 standard deviations (if data include negatives)
    # ylim.ref the two numbers in the two series to use as the reference point for converting them to indices
    #    when drawing on the page.  If both elements are 1, both series will start together at the left of the plot.
    # nbreaks is number of breaks in horizontal axis
    # lwd and mar are graphics parameters (see ?par)
    # colgrid is colour of gridlines; if NULL there are no gridlines
    # ylab1 and ylab2 are the labels for the two y axes
    # yleg1 and yleg2 are the labels for the two series in the legend
    # xlab and main are for x label and main title as in plot()
    # legx and legy are x and y position fed through to legend()
    # ... is parameters to pass to legend()
    # Note that default colours were chosen by colorspace::rainbow_hcl(2, c = 80, l = 50)

    # strip excess attributes (eg xts etc) from the two vertical axis variables
    ylab1 <- as.character(ylab1)
    ylab2 <- as.character(ylab2)
    y1 <- as.numeric(y1)
    y2 <- as.numeric(y2)

    # is ylim.ref is NULL, calculate a good default
    if(is.null(ylim.ref)){
        if (length(y1) == length(y2)){
            ylim.ref <- c(1, 1)
        } else {
            if (min(x1) >  min(x2)){
                ylim.ref <- c(1, which(abs(x2 - min(x1)) == min(abs(x2 - min(x1)))))
            } else {
                ylim.ref <- c(which(abs(x1 - min(x2)) == min(abs(x1 - min(x2)))), 1)
            }
        }


    }


    oldpar <- par(mar = mar)
    xbreaks <- round(seq(from = min(c(x1, x2)), to = max(c(x1, x2)), length.out = nxbreaks))

    # unless ylim1 or ylim2 were set, we set them to levels that make it equivalent
    # to a graphic drawn of indexed series (if all data positive), or to the mean
    # of each series +/- three standard deviations if some data are negative
    if(is.null(ylim1) & is.null(ylim2)){
        if(min(c(y1, y2), na.rm = TRUE) < 0){
            message("With negative values ylim1 or ylim2 need to be chosen by a method other than treating both series visually as though they are indexed. Defaulting to mean value +/- 3 times the standard deviations.")
            ylim1 <- c(-3, 3) * sd(y1, na.rm = TRUE) + mean(y1, na.rm = TRUE)
            ylim2 <- c(-3, 3) * sd(y2, na.rm = TRUE) + mean(y2, na.rm = TRUE)
        }


        if(ylim.ref[1] > length(y1)){
            stop("ylim.ref[1] must be a number shorter than the length of the first series.")
        }
        if(ylim.ref[2] > length(y2)){
            stop("ylim.ref[2] must be a number shorter than the length of the second series.")
        }

        if(!silent) message("The two series will be presented visually as though they had been converted to indexes.")

        # convert the variables to indexes (base value of 1 at the time specified by ylim.ref)
        ind1 <- as.numeric(y1) / y1[ylim.ref[1]]
        ind2 <- as.numeric(y2) / y2[ylim.ref[2]]

        # calculate y axis limits on the "index to 1" scale
        indlimits <- range(c(ind1, ind2), na.rm = TRUE)

        # convert that back to the original y axis scales
        ylim1 = indlimits * y1[ylim.ref[1]]
        ylim2 = indlimits * y2[ylim.ref[2]]
    } else {
        if(!silent) warning("You've chosen to set at least one of the vertical axes limits manually.  Up to you, but it is often better to leave it to the defaults.")
    }

    # draw first series - with no axes.
    plot(x1, y1, type = "l", axes = FALSE, lwd = lwd[1],
         xlab = xlab, ylab = "", col = col[1], main = main,
         xlim = range(xbreaks), ylim = ylim1)

    # add in the gridlines if wanted:
    if(!is.null(colgrid)){
        grid(lty = 1, nx = NA, ny = NULL, col = colgrid)
        abline(v = xbreaks, col = colgrid)
    }

    # add in the left hand vertical axis and its label
    axis(2, col = col[1], col.axis= col[1], las=1 )  ## las=1 makes horizontal labels
    mtext(paste0("\n", ylab1, "\n"), side = 2, col = col[1], line = 1.5)

    # Allow a second plot on the same graph
    par(new=TRUE)

    # Plot the second series:
    plot(x2, y2,   xlab="", ylab="", axes = FALSE, type = "l", lwd = lwd[2],
         col = col[2], xlim = range(xbreaks), ylim = ylim2)

    ## add second vertical axis (on right) and its label
    mtext(paste0("\n", ylab2, "\n"), side = 4, col = col[2], line = 4.5)
    axis(4,  col = col[2], col.axis = col[2], las=1)

    # Draw the horizontal time axis
    axis(1, at = xbreaks, labels = xbreaks)

    # Add Legend
    legend(x = legx, y = legy, legend=c(yleg1, yleg2),
           text.col = col, lty = c(1, 1), lwd = lwd, col = col,
           bty = bty, ...)

    par(oldpar)
}