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 dont see any references to font
size in the code. Digitize changes the number size on the x-axis, but dont
see a corresponding way of making the labeling size smaller.
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))
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