The color of the squares is also currently hard coded.
The thing is, there are so many different elements to a forest plot
(squares, lines, polygons, text, axes, axis labels, etc.), if I would add
arguments to set the color of each element, things would really get out of
hand (as far as I am concerned, there are already too many arguments to
begin with). I can think of one possibility: I could allow the col argument
to accept a vector of colors and then apply the different elements of that
vector to the various elements in the plot. Of course, there is also a limit
to how far that can be taken. For example, what if somebody wants to have a
different color for *one* of the squares and a different color for the other
squares?
Another possibility is to do some post-processing with other software. One
can create the forest plot in R, save it for example as a postscript file,
and the edit the plot in other software. Yes, I prefer it if I can create
the plot in R and have it exactly the way I want it (without having to do
any post-processing), but sometimes that may not be possible.
Note that you can always add whatever you want to a plot created by the
forest() function after it has been drawn. You can add text, lines, squares,
polygons, whatever in any color you desire (e.g., with the text(),
segments(), points(), polygon() functions). So, you could also just plot
over the squares with:
points(yi, 4:1, pch=15, col="red")
To get rid of the black squares that are drawn by the forest function, add
psize=0 as an argument in forest() (this will make the size of squares equal
to 0, so essentially, they are invisible).
If you want to make the size of the points inversely proportional to some
function of the precision of the estimates, use points() together with the
cex argument. For example:
wi<- 1/sqrt(vi)
psize<- wi/sum(wi)
psize<- (psize - min(psize)) / (max(psize) - min(psize))
psize<- (psize * 1.0) + 0.5
points(yi, 4:1, pch=15, col="red", cex=psize)
Best,
Wolfgang
-----Original Message-----
From: Paola Tellaroli [mailto:[hidden
email]<http://user/SendEmail.jtp?type=node&node=3768683&i=0>]
Sent: Thursday, August 25, 2011 10:57
To: Viechtbauer Wolfgang (STAT)
Cc: [hidden email]<http://user/SendEmail.jtp?type=node&node=3768683&i=1>;
Bernd Weiss
Subject: Re: [R] Change color in forest.rma (metafor)
Thank you for your attention and help!
In this way I get the diamond coloured, but actually I would have the
squares representing the values of the individual studies coloured. Is
it
somehow possible?
Paola
2011/8/24 Viechtbauer Wolfgang (STAT)
<[hidden email]<http://user/SendEmail.jtp?type=node&node=3768683&i=2>>
Thank you, Bernd, for looking into this.
Yes, at the moment, the color of the summary estimate for models without
moderators is hard-coded (as black). I didn't think people may want to
change that. I guess I was wrong =)
A dirty solution for the moment is to add:
addpoly(dfs, efac=6, row=-1, col="red", border="red", annotate=F,
mlab="")
after the call to forest(). You will get a warning message (since the
border argument gets passed to the text() function inside addpoly() and
that's not a par for text), but you can just ignore that.
Best,
--
Wolfgang Viechtbauer
Department of Psychiatry and Neuropsychology
School for Mental Health and Neuroscience
Maastricht University, P.O. Box 616
6200 MD Maastricht, The Netherlands
Tel: +31 (43) 368-5248
Fax: +31 (43) 368-8689
Web: http://www.wvbauer.com
-----Original Message-----
From: Bernd Weiss [mailto:[hidden
email]<http://user/SendEmail.jtp?type=node&node=3768683&i=3>]
Sent: Wednesday, August 24, 2011 16:22
To: Paola Tellaroli
Cc: [hidden email]<http://user/SendEmail.jtp?type=node&node=3768683&i=4>;
[hidden email]<http://user/SendEmail.jtp?type=node&node=3768683&i=5>
Subject: Re: [R] Change color in forest.rma (metafor)
Am 24.08.2011 07:50, schrieb Paola Tellaroli:
My script is the following:
library(metafor)
yi<-c(-0.1, 0.2, 0.3, 0.4)
sei<-c(0.4, 0.2, 0.6, 0.1)
vi<-sei^2
studi<-c("A", "B", "C", "D")
eventi.c<-c(10, 5, 7, 6)
n.c<-c(11, 34, 25, 20)
eventi.a<-c(2, 7, 6, 5)
n.a<-c(11, 35, 25, 15)
dfs<-rma(yi, vi, method="DL")
dfs
windows(height=6, width=10, pointsize=10)
windowsFonts(B=windowsFont("Bookman Old Style"))
forest.rma(dfs, slab=studi, xlim=c(-15, 10), ilab=cbind(eventi.c,
n.c,
eventi.a, n.a), ilab.xpos=c(-9.5, -8, -6, -4.5), cex=1.2, at=c(-2,
-1,
0, 1,
2), family="B", xlab="Hazard Ratio (log scale)", mlab="Random
Effects
Model", efac=5, col="red", border="red")
text(-10, -1.3, paste("Heterogeneity: I-squared=",
paste(paste(round(dfs$I2,
2), "%", sep=""), paste("p", round(dfs$QEp, 4), sep="="), sep=", "),
sep=""), font=4, cex=1.2, family="B")
op<-par(cex=1.2, font=2, family="B", oma=c(0.5, 0.5, 0.5, 0.5),
mar=c(0.5,
0.5, 0.5, 0.5))
text(x=c(-9.5, -8, -6, -4.5), 6, c("Events", "N", "Events", "N"),
cex=1.2 )
text(c(-8.7, -5.5, 8), 6.5, c("S", "A", "Log"))
text(-15, 6, "Trials", pos=4)
text(10, 6, "Hazard Ratio [95% CI]", pos=2)
par(op)
Even if I have specified "col="red", border="red"", color of squares
and
diamond rests black! Why?
As far as I know, "col" and "border" do only affect the fitted values
("diamonds"), i.e. the FEM/REM estimators (see ?forest.rma: "col:
character string specifying the name of a color to use for _the
fitted_
values ('"darkgray"' by default).")
Furthermore, I had a quick look at the source code and it might be a
bug. If I replace in line 2770 the line
cex * efac), col = "black", ...)
with
cex * efac), col = col, ...)
you can at least specify your own colour. Changing the border color
seems a bit more tricky...
However, Wolfgang Viechbauer (the package author) is always a very
responsive and helpful person and I suggest you better wait for his
answer.
Bernd
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