I lied, that was not my last question: how can I add two arrows at the bottom with the words "in favor of A / B"? This is not specified in the pdf and with "text" I have the impression that I can't add text below the x-axis.
2011/8/26 Paola Tellaroli <paola.tellar...@gmail.com> > Dear Prof. Viechtbauer, > thank you so much for your help and kindness. > > Clearly graphs are the minor problem in our work, and the parameters and > options that can vary in R are so many that it is obvious that you can not > expect > to change everything you want! > > Your suggestions are very helpuf, but I have one last question. I'm trying > to copy the style of a forest plot that I've seen and I like (the one in the > attached file, page 1034): can I do this in R? > > Best wishes, > > *Paola* > > > > 2011/8/25 Viechtbauer Wolfgang (STAT)-2 [via R] < > ml-node+3768683-1225159815-262...@n4.nabble.com> > >> 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 >> >> ______________________________________________ >> [hidden email] <http://user/SendEmail.jtp?type=node&node=3768683&i=6>mailing >> list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://r.789695.n4.nabble.com/Change-color-in-forest-rma-metafor-tp3765090p3768683.html >> To unsubscribe from Change color in forest.rma (metafor), click >> here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3765090&code=cGFvbGEudGVsbGFyb2xpQGdtYWlsLmNvbXwzNzY1MDkwfDQzMzczMjk1Ng==>. >> >> > > -- View this message in context: http://r.789695.n4.nabble.com/Change-color-in-forest-rma-metafor-tp3765090p3770899.html Sent from the R help mailing list archive at Nabble.com. 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