Hi All,
I have been able to modify the x-axis to start at zero by adding xlow
and xhigh parameters; that was pretty simple. I have been unable to
find the location of the code that would turn off the information
weighting of the box size (I have smaller randomized trials getting
less weight than a much larger non-randomized trial). The function
is forestplot() from rmeta.
Thanks for any help.
Gerard
Slightly modified working function with data and a call follows:
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,
...)
{
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
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()
}
tabletext<-cbind(c("","Randomized Trials"," Study 1", " Study 2",
" Combined", "", "Study 3 ", " Comorbid"," Non-Comorbid",""),
c("","","","","","","","","",""))
m <- c(NA, NA, 2.32 , 2.55 , 2.41 , NA, NA, 2.04 , 1.62 , NA)
l <- c(NA, NA, 1.1746, 1.1495, 1.4377, NA, NA, 1.609, 1.339, NA)
u <- c(NA, NA, 4.5919, 5.6364, 4.0490, NA, NA, 2.592, 1.952, NA)
fplot(tabletext, m, l ,u, zero=1, is.summary=c(rep(FALSE,3)),
clip=c(0,8), xlog=FALSE,
xlow=0, xhigh=6, xlab="Odds Ratio",digitsize=0.9,graphwidth =
unit(4,"inches"),
col=meta.colors(box="black",line="black", summary="black"))
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