R help - Jul 2013 - Greek symbols in study labels and custom summary lines in forest plot (meta)

Dear R helpers,

Is there a way to display mathematical notations (e.g. greek characters,
subscripts) properly in study (studlab) and group (byvar) labels in a forest
plot created using the meta package?

#Example:
library(meta)
logHR <- log(runif(10,0.5,2))
selogHR <- log(runif(10,0.05,0.2))
study=c(0.1,.2,.3,.4,.5,0.1,.2,.3,.4,.5)
group=c(rep('alpha',5),rep('beta',5))
meta1=metagen(logHR, selogHR,
sm="HR",studlab=paste("Fixed",expression(beta[w]),study),byvar=group)
forest(meta1, print.byvar=F)

Question 2
Is there a way to add a line to this plot at my preferred location? For example,
I want to add a within-group combined estimate line (the default here is just an
overall group line by random or fixed effects).
I know I need to use grid.lines, e.g.

grid.lines(x = 3, y = c(0.5,1),gp = gpar(col = 5))

But for the life of me I can't work out the co-ordinate system in grid
graphics!

Thank you for ANY help or tips! I've run out of things to try :(

Eleni

Eleni Rapsomaniki
Research Associate/Statistics, PhD
Clinical Epidemiology Group
Department of Epidemiology and Public Health 
University College London Medical School

On Jul 29, 2013, at 11:52 AM, Rapsomaniki, Eleni wrote:
> Dear R helpers,
> 
> Is there a way to display mathematical notations (e.g. greek characters,
subscripts) properly in study (studlab) and group (byvar) labels in a forest
plot created using the meta package?
> 
> #Example:
> library(meta)
> logHR <- log(runif(10,0.5,2))
> selogHR <- log(runif(10,0.05,0.2))
> study=c(0.1,.2,.3,.4,.5,0.1,.2,.3,.4,.5)
> group=c(rep('alpha',5),rep('beta',5))
> meta1=metagen(logHR, selogHR,
sm="HR",studlab=paste("Fixed",expression(beta[w]),study),byvar=group)
> forest(meta1, print.byvar=F)
I tried a variety of plotmath and substitute strategies but the arguments to
studlab get first processed with 'as.character' and then put into a
data.frame before printing. Dataframes do not accept language objects, so R
expressions could not be processed.
> dftest <- data.frame(a =expression(a,b,c))
Error in as.data.frame.default(x[[i]], optional = TRUE) : 
  cannot coerce class ""expression"" to a data.frame


Best I could to was '

   ... ,studlab=paste('Fixed ?[w]=',study), ....
> 
> Question 2
> Is there a way to add a line to this plot at my preferred location? For
example, I want to add a within-group combined estimate line (the default here
is just an overall group line by random or fixed effects).
> I know I need to use grid.lines, e.g.
> 
> grid.lines(x = 3, y = c(0.5,1),gp = gpar(col = 5))
> 
> But for the life of me I can't work out the co-ordinate system in grid
graphics!
Unfortunately all of the printing to the device is handled inside the
'forest' function and no list representation is returned as a value to
be augmented and later printed. So the input data would need to be entered in a
manner that gets processed as text or you would need to modify the code. I
don't have the knowledge of the meta package that can get there.

-- 
David Winsemius
Alameda, CA, USA