package metafor: error when setting 'col' and 'at' for a forest plot
Brilliant, this works very well. Thank you for explaining this so clearly, all your points are well taken. Sincerely, Brian Brian Z Ring PhD Professor, Director Institute of Personalized and Genomic Medicine College of Life Science Huazhong University of Science and Technology Wuhan, ?China -----Original Message----- From: Viechtbauer Wolfgang (STAT) [mailto:wolfgang.viechtbauer at maastrichtuniversity.nl] Sent: Monday, January 07, 2013 6:16 PM To: Brian Z Ring; 'David Winsemius'; r-help at r-project.org Subject: RE: [R] package metafor: error when setting 'col' and 'at' for a forest plot Dear Brian, At the moment, the various forest() functions are not meant to accept 'col' as an argument. While it is indeed possible to specify a 'col' argument, it will be passed on via the ... argument to further functions within forest() and this is where things can go awry. To give a more technical explanation, let's look at your example. First, note that the highest 'at' value you specified is log(10), which is approximately 2.30. However, the highest upper CI bound in your dataset is 2.9. Therefore, the forest() function wants to draw a right-pointed arrow for that study using the polygon() function. The code within forest() looks something like this: polygon(<lots of other stuff>, col="black", ...) When you specify a 'col' argument, it is passed on to polygon() via ... -- but col="black" is already hard-coded in forest() and so you get the "formal argument "col" matched by multiple actual arguments" error. The issue of changing colors in the forest() functions has come up before: https://stat.ethz.ch/pipermail/r-help/2011-August/287788.html In fact, the problems associated with allowing the user to specify colors in high-level plotting functions, such as forest(), was nicely discussed in a recent article by Paul Murrell in the R Journal: http://journal.r-project.org/archive/2012-2/RJournal_2012-2_Murrell.pdf I may add functionality to the forest() functions to handle a 'col' argument for specifying row colors, but I will have to evaulate carefully how well that will work. Also, I would then need to change the current 'col' argument in the forest.rma() function -- breaking backwards compatability :/ Back to your example. You can actually get it to work if you use: forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High, at=log(c(.05, .25, 1, 20)), slab=forest$SNP, atransf=exp) in which case the values of 'at' encompass the CI bounds of all studies. Then the forest() function does not use polygon(), but segments() and here 'col' is not hard-coded. One (probably) unintended consequence of using 'col' this way is that the x axis label is also given a different color. A few other notes: 1) Calling your data frame 'forest' is probably not a good idea -- since that is the name of a function. 2) Your data appear to be (raw -- not log transformed) odds ratios and the corresponding CI bounds. So, you should not be using the atransf arguments -- or you would be transforming your odds ratios to exp(ORs). Probably closer to what you want is: dat <- read.table(header=TRUE, text=" SNP Group High Low OR rs1137101 A 1.21 0.87 1.03 rs1137101 B 2.11 1.21 1.6 rs1137101 C 2.9 1.42 2.03 rs1042522 A 1.12 0.84 0.97 rs1042522 B 1.15 0.79 0.95 rs1042522 C 0.92 0.5 0.7 rs1625895 A 1.14 0.76 0.93 rs1625895 B 1.15 0.75 0.93 rs1625895 C NA NA NA ACEI/D A 1.55 0.79 1.11 ACEI/D B 1.25 0.76 0.98 ACEI/D C 0.85 0.41 0.59 ") forest(dat$OR, ci.lb=dat$Low, ci.ub=dat$High, col=c(1,2,3), at=c(.25, 1, 2, 3), slab=dat$SNP, refline=1, xlab=" ", xlim=c(-1.5,5.5)) mtext("Odds Ratio", side=1, line=2.5, adj=0.45) where I manually add the x axis label, so that it is in black. Again, though, using 'col' this way is technically not intended (even though it does work here). I hope this helps! Best, Wolfgang -- Wolfgang Viechtbauer, Ph.D., Statistician Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com
-----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Brian Z Ring Sent: Sunday, January 06, 2013 05:48 To: 'David Winsemius'; r-help at r-project.org Subject: Re: [R] package metafor: error when setting 'col' and 'at' for a forest plot Good suggestion, and yes, the given examples work. Using a modification of one of the supplied examples, where in the final line I only added the parameter col=c(1,2,3): data(dat.bcg) dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg, append=TRUE) forest(dat$yi, dat$vi, slab=paste(dat$author, dat$year, sep=", "), atransf=exp, at=log(c(.05,.25,1,4,20)), col=c(1,2,3)) I get a plot similar to what I want to achieve. My code: forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High, col=c(1,2,3), at=log(c(.05, .25, 1, 10)), slab=forest$SNP, atransf=exp) differs in the data and using confidence intervals instead of vi (sample variance). The parameters being changed in my line of code are fairly simple, just color of each row and the x axis tick marks. Setting each of these independently with my data works fine, it's only when I try to do both that it fails. I'm still stuck. Here is some example data that should reproduce the error: SNP Group High Low OR rs1137101 A 1.21 0.87 1.03 rs1137101 B 2.11 1.21 1.6 rs1137101 C 2.9 1.42 2.03 rs1042522 A 1.12 0.84 0.97 rs1042522 B 1.15 0.79 0.95 rs1042522 C 0.92 0.5 0.7 rs1625895 A 1.14 0.76 0.93 rs1625895 B 1.15 0.75 0.93 rs1625895 C NA NA NA ACEI/D A 1.55 0.79 1.11 ACEI/D B 1.25 0.76 0.98 ACEI/D C 0.85 0.41 0.59 -----Original Message----- From: David Winsemius [mailto:dwinsemius at comcast.net] Sent: Sunday, January 06, 2013 2:31 AM To: Brian Z Ring Cc: r-help at r-project.org Subject: Re: [R] package metafor: error when setting 'col' and 'at' for a forest plot On Jan 4, 2013, at 9:13 PM, Brian Z Ring wrote:
I am using metafor to create forest plots. This code gives me the expected plot (setting x axis tick marks): forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High, at=log(c(. 05, .25, 1, 10)), slab=forest$SNP, atransf=exp) As does this (setting colors): forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High, col=c(1,2,3), slab=forest$SNP, atransf=exp) But if I try to set both 'at' and 'col': forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High, col=c(1,2,3), at=log(c(.05, .25, 1, 10)), slab=forest$SNP, atransf=exp) I receive this error: Error in polygon(x = c(alim[2], alim[2] - (1.4/100) * cex * (xlim[2] - : formal argument "col" matched by multiple actual arguments Any help greatly appreciated.
Can you reproduce this using the examples in the package help pages? -- David Winsemius, MD Alameda, CA, USA
______________________________________________ R-help at r-project.org 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.