[R] package metafor: error when setting 'col' and 'at' for a forest plot

[Brian Z Ring]

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