R/forestplot.boxcol.R

In foramashar/fashaR: R package with Foram's functions

#' Modified forestplot function to allow for different colored
#' boxes 
#'
#' @return Graphical output
#'
#' @seealso rmeta, forestplot
#' @export
#' @examples
#' forestplot.new(as.matrix(blah), mean=test.or, lower=test.l, upper=test.u, zero=1, 
#' is.summary=c(rep(c(T, rep(F,4)),3),T),
#' col=meta.colors(box=c(NA, rep("royalblue",4),NA,rep("red",4),NA, rep("purple3",4)),lines=c("grey","red"), summary="black"))

forestplot.boxcol=
function (labeltext, mean, lower, upper, align = NULL, is.summary = FALSE,
    clip = c(-Inf, Inf), xlab = "", zero = 0, graphwidth = unit(2,
        "inches"), col = meta.colors(), xlog = FALSE, xticks = NULL,
    boxsize = NULL, ...)
{
    require("grid") || stop("`grid' package not found")
    require("rmeta") || stop("`rmeta' package not found")
    drawNormalCI <- function(LL, OR, UL, size, testcol) {
        size = 0.75 * size
        clipupper <- convertX(unit(UL, "native"), "npc", valueOnly = TRUE) >
            1
        cliplower <- convertX(unit(LL, "native"), "npc", valueOnly = TRUE) <
            0
        box <- convertX(unit(OR, "native"), "npc", valueOnly = TRUE)
        clipbox <- box < 0 || box > 1
        if (clipupper || cliplower) {
            ends <- "both"
            lims <- unit(c(0, 1), c("npc", "npc"))
            if (!clipupper) {
                ends <- "first"
                lims <- unit(c(0, UL), c("npc", "native"))
            }
            if (!cliplower) {
                ends <- "last"
                lims <- unit(c(LL, 1), c("native", "npc"))
            }
            grid.lines(x = lims, y = 0.5, arrow = arrow(ends = ends,
                length = unit(0.05, "inches")), gp = gpar(col = col$lines))
            if (!clipbox)
                grid.rect(x = unit(OR, "native"), width = unit(size,
                  "snpc"), height = unit(size, "snpc"), gp = gpar(fill = testcol,
                  col = testcol))
        }
        else {
            grid.lines(x = unit(c(LL, UL), "native"), y = 0.5,
                gp = gpar(col = col$lines))
            grid.rect(x = unit(OR, "native"), width = unit(size,
                "snpc"), height = unit(size, "snpc"), gp = gpar(fill = testcol,
                col = testcol))
            if ((convertX(unit(OR, "native") + unit(0.5 * size,
                "lines"), "native", valueOnly = TRUE) > UL) &&
                (convertX(unit(OR, "native") - unit(0.5 * size,
                  "lines"), "native", valueOnly = TRUE) < LL))
                grid.lines(x = unit(c(LL, UL), "native"), y = 0.5,
                  gp = gpar(col = col$lines))
        }
    }
    drawSummaryCI <- function(LL, OR, UL, size) {
        grid.polygon(x = unit(c(LL, OR, UL, OR), "native"), y = unit(0.5 +
            c(0, 0.5 * size, 0, -0.5 * size), "npc"), gp = gpar(fill = col$summary,
            col = col$summary))
    }
    plot.new()
    widthcolumn <- !apply(is.na(labeltext), 1, any)
    nc <- NCOL(labeltext)
    labels <- vector("list", nc)
    if (is.null(align))
        align <- c("l", rep("r", nc - 1))
    else align <- rep(align, length = nc)
    nr <- NROW(labeltext)
    is.summary <- rep(is.summary, length = nr)
    for (j in 1:nc) {
        labels[[j]] <- vector("list", nr)
        for (i in 1:nr) {
            if (is.na(labeltext[i, j]))
                next
            x <- switch(align[j], l = 0, r = 1, c = 0.5)
            just <- switch(align[j], l = "left", r = "right",
                c = "center")
            labels[[j]][[i]] <- textGrob(labeltext[i, j], x = x,
                just = just, gp = gpar(fontface = if (is.summary[i])
                  "bold"
                else "plain", col = rep(col$text, length = nr)[i]))
        }
    }
    colgap <- unit(3, "mm")
    colwidths <- unit.c(max(unit(rep(1, sum(widthcolumn)), "grobwidth",
        labels[[1]][widthcolumn])), colgap)
    if (nc > 1) {
        for (i in 2:nc) colwidths <- unit.c(colwidths, max(unit(rep(1,
            sum(widthcolumn)), "grobwidth", labels[[i]][widthcolumn])),
            colgap)
    }
    colwidths <- unit.c(colwidths, graphwidth)
    pushViewport(viewport(layout = grid.layout(nr + 1, nc * 2 +
        1, widths = colwidths, heights = unit(c(rep(1, nr), 0.5),
        "lines"))))
    cwidth <- (upper - lower)
    xrange <- c(max(min(lower, na.rm = TRUE), clip[1]), min(max(upper,
        na.rm = TRUE), clip[2]))
    info <- 1/cwidth
    info <- info/max(info[!is.summary], na.rm = TRUE)
    info[is.summary] <- 1
    if (!is.null(boxsize))
        info <- rep(boxsize, length = length(info))
    for (j in 1:nc) {
        for (i in 1:nr) {
            if (!is.null(labels[[j]][[i]])) {
                pushViewport(viewport(layout.pos.row = i, layout.pos.col = 2 *
                  j - 1))
                grid.draw(labels[[j]][[i]])
                popViewport()
            }
        }
    }
    pushViewport(viewport(layout.pos.col = 2 * nc + 1, xscale = xrange))
    grid.lines(x = unit(zero, "native"), y = 0:1, gp = gpar(col = col$zero))
    if (xlog) {
        if (is.null(xticks)) {
            ticks <- pretty(exp(xrange))
            ticks <- ticks[ticks > 0]
        }
        else {
            ticks <- xticks
        }
        if (length(ticks)) {
            if (min(lower, na.rm = TRUE) < clip[1])
                ticks <- c(exp(clip[1]), ticks)
            if (max(upper, na.rm = TRUE) > clip[2])
                ticks <- c(ticks, exp(clip[2]))
            xax <- xaxisGrob(gp = gpar(cex = 0.6, col = col$axes),
                at = log(ticks), name = "xax")
            xax1 <- editGrob(xax, gPath("labels"), label = format(ticks,
                digits = 2))
            grid.draw(xax1)
        }
    }
    else {
        if (is.null(xticks)) {
            grid.xaxis(gp = gpar(cex = 0.6, col = col$axes))
        }
        else if (length(xticks)) {
            grid.xaxis(at = xticks, gp = gpar(cex = 0.6, col = col$axes))
        }
    }
    grid.text(xlab, y = unit(-2, "lines"), gp = gpar(col = col$axes))
    popViewport()
    for (i in 1:nr) {
        if (is.na(mean[i]))
            next
        pushViewport(viewport(layout.pos.row = i, layout.pos.col = 2 *
            nc + 1, xscale = xrange))
        if (is.summary[i])
            drawSummaryCI(lower[i], mean[i], upper[i], info[i])
        else drawNormalCI(lower[i], mean[i], upper[i], info[i], col$box[i])
        popViewport()
    }
    popViewport()
}