[R] changing font size in Forest plot code.
David Winsemius
dwinsemius at comcast.net
Sun Jan 19 23:16:24 CET 2014
On Jan 19, 2014, at 1:13 PM, Gerard Smits wrote:
> Hi All,
>
> I have pulled the following function (fplot) from the internet, and unfortunately I do not see an author to whom I can give credit. It used grid graphics and relies mostly on package rmeta by Thomas Lumley. I am trying to make the font smaller in my labeltext, but don‚t see any references to font size in the code. Digitize changes the number size on the x-axis, but don‚t see a corresponding way of making the labeling size smaller.
>
Wouldn't it just be needed to specify grid parameters (as exemplified several other places in that code) in the code where 'labels' are created?
...
labels[[j]][[i]] <- textGrob(labeltext[i, j], x = x,
just = just, gp = gpar(fontsize=8, fontface = if (is.summary[i]) "bold"
else "plain", col = rep(col$text, length = nr)[i]))
...
Seems to succeed (once the errant and quite strange double comma character '„' is removed and replaced with a proper double quote.) If you are doing this on a word processor, then you should convert to a programming text editor.
--
David.
> Using R 3.0.2
>
> Any suggestions appreciated.
>
> Gerard Smits
>
> fplot=function (labeltext, mean, lower, upper, align = NULL, is.summary = FALSE,
> clip = c(-Inf, Inf), xlab = "", zero = 1, graphwidth = unit(3,"inches"),
> col = meta.colors(), xlog = FALSE, xticks = NULL,
> xlow=0, xhigh, digitsize, boxsize,
> ...)
>
> {
> require("grid") || stop("`grid' package not found")
> require("rmeta") || stop("`rmeta' package not found")
>
>
> drawNormalCI <- function(LL, OR, UL, size)
> {
>
> size = 0.75 * size
> clipupper <- convertX(unit(UL, "native"), "npc", valueOnly = TRUE) > 1
> cliplower <- convertX(unit(LL, "native"), "npc", valueOnly = TRUE) < 0
> box <- convertX(unit(OR, "native"), "npc", valueOnly = TRUE)
> clipbox <- box < 0 || box > 1
>
> if (clipupper || cliplower)
> {
> ends <- "both"
> lims <- unit(c(0, 1), c("npc", "npc"))
> if (!clipupper) {
> ends <- "first"
> lims <- unit(c(0, UL), c("npc", "native"))
> }
> if (!cliplower) {
> ends <- "last"
> lims <- unit(c(LL, 1), c("native", "npc"))
> }
> grid.lines(x = lims, y = 0.5, arrow = arrow(ends = ends,
> length = unit(0.05, "inches")), gp = gpar(col = col$lines))
>
> if (!clipbox)
> grid.rect(x = unit(OR, "native"), width = unit(size,
> "snpc"), height = unit(size, "snpc"), gp = gpar(fill = col$box,
> col = col$box))
> }
> else {
> grid.lines(x = unit(c(LL, UL), "native"), y = 0.5,
> gp = gpar(col = col$lines))
> grid.rect(x = unit(OR, "native"), width = unit(size,
> "snpc"), height = unit(size, "snpc"), gp = gpar(fill = col$box,
> col = col$box))
> if ((convertX(unit(OR, "native") + unit(0.5 * size,
> "lines"), "native", valueOnly = TRUE) > UL) &&
> (convertX(unit(OR, "native") - unit(0.5 * size,
> "lines"), "native", valueOnly = TRUE) < LL))
> grid.lines(x = unit(c(LL, UL), "native"), y = 0.5,
> gp = gpar(col = col$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$text, length = nr)[i]))
> }
> }
> colgap <- unit(3, "mm")
> colwidths <- unit.c(max(unit(rep(1, sum(widthcolumn)), "grobwidth",
> labels[[1]][widthcolumn])), colgap)
> if (nc > 1) {
> for (i in 2:nc) colwidths <- unit.c(colwidths, max(unit(rep(1,
> sum(widthcolumn)), "grobwidth", labels[[i]][widthcolumn])),
> colgap)
> }
> colwidths <- unit.c(colwidths, graphwidth)
> pushViewport(viewport(layout = grid.layout(nr + 1, nc * 2 +
> 1, widths = colwidths, heights = unit(c(rep(1, nr), 0.5),
> "lines"))))
> cwidth <- (upper - lower)
>
> #xrange <- c(max(min(lower, na.rm = TRUE), clip[1]), min(max(upper, na.rm = TRUE), clip[2]))
> xrange <- c(xlow,xhigh)
>
> info <- 1/cwidth
> info <- info/max(info[!is.summary], na.rm = TRUE)
> info[is.summary] <- 1
>
> if (!is.null(boxsize))
> info <- rep(boxsize, length = length(info))
>
> for (j in 1:nc) {
> for (i in 1:nr) {
> if (!is.null(labels[[j]][[i]])) {
> pushViewport(viewport(layout.pos.row = i, layout.pos.col = 2 *
> j - 1))
> grid.draw(labels[[j]][[i]])
> popViewport()
> }
> }
> }
>
> pushViewport(viewport(layout.pos.col = 2 * nc + 1, xscale = xrange))
> grid.lines(x = unit(zero, "native"), y = 0:1, gp = gpar(col = col$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 = digitsize, col = col$axes),
> at = log(ticks), name = "xax")
> xax1 <- editGrob(xax, gPath("labels"), label = format(ticks, digits = 2))
> grid.draw(xax1)
> }
> }
> else {
> if (is.null(xticks)) {
> grid.xaxis(gp = gpar(cex = digitsize, col = col$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])
> popViewport()
> }
> popViewport()
> }
>
>
>
> # my code starts here:
>
>
> labletext<-cbind(c("",
> "All Available Eyes (n=194)",
> "",
> "Month 12 Visit Timing (p=0.8312*)",
> " Before Window (n=12)",
> " In Window (n=146)",
> " After Window (n=36)",
> "",
> "Major Protocol Deviation (p=0.5189*)",
> " None (n=149)",
> " Present (n=45)",
> "",
> "Protocol Approved Device (p=0.5131*)",
> " Yes (n=62)",
> " No (n=132)",
> "",
> "ITT Imputations",
> " Multiple Imputation (n=210)",
> " LOCF (n=210)",
> " Worst Case (n=210)"
> ),
>
> c("",
> " 0.0309 [-0.0488 0.1106]",
> "","",
> "","","","","",
> "","","","","",
> "","","","","",
> "",""))
>
>
> m <- c(NA, 0.0309, NA, NA, 0.1591, 0.0286, 0.0153, NA, NA, 0.0529, -0.0441, NA, NA, 0.0364, 0.0455, NA, NA, 0.0123, -0.0667, -0.1429)
> l <- c(NA, -0.0488, NA, NA, -0.0524, -0.0548, -0.1372, NA, NA, -0.0251, -0.2106, NA, NA, -0.0529, -0.0605, NA, NA, -0.0670, -0.2333, -0.2576)
> u <- c(NA, 0.1106, NA, NA, 0.3706, 0.1120, 0.1678, NA, NA, 0.1309, 0.1224, NA, NA, 0.1257, 0.1515, NA, NA, 0.0916, 0.1000, -0.0282)
>
>
> fplot(labletext, m, l ,u, zero=0, is.summary=c(rep(FALSE,3)), clip=c(0,8), xlog=FALSE,
> xlow=-0.5, xhigh=+0.5, xlab=„\nVariable Tested", digitsize=0.9, graphwidth = unit(3,"inches"),
> boxsize=.6,
> col=meta.colors(box="blue",line="blue", summary="red"))
>
> grid.text("Forest Plot of xxx\nwith Point Estimate and 95% CI", x = .5, y = .9, gp=gpar(fontsize=15))
> grid.text("* Test of heterogeneity of subgroups using General Estimating Equation model.", x = .38, y = .07, gp=gpar(fontsize=10))
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
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