### Table of Contents

## Forest Plot with Superscripts

### Description

Some journals require reference numbers to be shown in forest plots (in addition to the study authors and publication years). Typically, the reference numbers are supposed to be shown as superscripts. How to accomplish this with R and the metafor package has occasionally been asked. Text involving superscripts can be added to plots using 'expressions', which are more generally used to add mathematical equations to plots. See `help(plotmath)`

for the syntax to create such mathematical expressions. An additional difficulty in the present context is that one typically wants to substitute variables (like the reference numbers) into these expressions. This can be accomplished in various ways using functions such as `substitute()`

and `bquote()`

. Below is an example to illustrate how this can be done to add reference numbers as superscripts and additional information from the random-effects model to a forest plot.

### Plot

### Code

### copy BCG vaccine meta-analysis data into 'dat' dat <- dat.bcg ### calculate log risk ratios and corresponding sampling variances dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat) ### create study labels dat$slab <- with(dat, paste(author, year, sep=", ")) ### combine study labels with trial numbers in superscripts dat$slab.ref <- mapply(function(x,y) as.expression(bquote(.(x)^.(y))), dat$slab, dat$trial) ### fit random-effects model res <- rma(yi, vi, data=dat) ### a little helper function to add Q-test, I^2, and tau^2 estimate info mlabfun <- function(text, x) { list(bquote(paste(.(text), " (Q = ", .(fmtx(x$QE, digits=2)), ", df = ", .(x$k - x$p), ", ", .(fmtp(x$QEp, digits=3, pname="p", add0=TRUE, sep=TRUE, equal=TRUE)), "; ", I^2, " = ", .(fmtx(x$I2, digits=1)), "%, ", tau^2, " = ", .(fmtx(x$tau2, digits=2)), ")")))} ### forest plot with extra annotations forest(res, atransf=exp, at=log(c(0.05, 0.25, 1, 4)), xlim=c(-16,6), ilab=cbind(tpos, tneg, cpos, cneg), ilab.lab=c("TB+","TB-","TB+","TB-"), ilab.xpos=c(-9.5,-8,-6,-4.5), cex=0.75, header="Author(s) and Year", mlab=mlabfun("RE Model", res), slab=slab.ref, shade=TRUE) text(c(-8.75,-5.25), res$k+3, c("Vaccinated", "Control"), cex=0.75, font=2)