Thank you so much!!! Could you tell me also how to change the size of the chart? There is not enough space below the chart to add the arrows!
2011/8/28 Uwe Ligges-3 [via R] < ml-node+3774557-1567708350-262...@n4.nabble.com> > > > On 26.08.2011 15:50, Paola Tellaroli wrote: > > 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. > > You can, see ?par and its "xpd" argument. > > Uwe Ligges > > > > > > > > > 2011/8/26 Paola Tellaroli<[hidden > > email]<http://user/SendEmail.jtp?type=node&node=3774557&i=0>> > > > > >> 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]< > >> [hidden email] <http://user/SendEmail.jtp?type=node&node=3774557&i=1>> > >> > >>> 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: > >>> > >>> > > >>> > >>> > >> > >> > > > > > > -- > > 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. > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > [hidden email] > > <http://user/SendEmail.jtp?type=node&node=3774557&i=2>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. > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=3774557&i=3>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-tp3765090p3774557.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-tp3765090p3775946.html Sent from the R help mailing list archive at Nabble.com. 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