[R-meta] meta-regression scatterplot in ggplot2: code
Emerson M. Del Ponte
delponte @ending from ufv@br
Thu May 24 21:38:37 CEST 2018
Dear Moritz
As a ggplot user, I tried to use your code and got the same issues as
Wolfgang. Can you send a fully reproducible code and the link to see the
plot that you obtained using your code?
Cheers,
Emerson
Emerson Medeiros Del Ponte
Associate Professor & Graduate Studies Chair
Departamento de Fitopatologia, Universidade Federal de Viçosa
Viçosa MG Brasil +55 (31) 3899-1103
-------------------------------------------------------------
Editor in Chief for Tropical Plant Pathology
www.sbfitopatologia.org/tpp
@TropPlantPathol
Em qui, 24 de mai de 2018 às 15:49, Viechtbauer, Wolfgang (SP) <
wolfgang.viechtbauer using maastrichtuniversity.nl> escreveu:
> Dear Moritz,
>
> Thanks for the code. Unfortunately, it doesn't work for me. One problem
> are the curly quotes (“) that R won't like. Also, 'sizex' needs to be
> defined first. But after fixing that, this can't work. If I run:
>
> ggplot(plot.dat, aes(ablat, exp(yi)))
> + geom_point(pch = 19, cex = 1.5 * sizex)
>
> then this is interpreted as two separate commands. This would work:
>
> ggplot(plot.dat, aes(ablat, exp(yi))) +
> geom_point(pch = 19, cex = 1.5 * sizex)
>
> Then I also got:
>
> Error in log_trans() : could not find function "log_trans"
>
> At that point, I kind of gave up.
>
> Best,
> Wolfgang
>
> -----Original Message-----
> From: R-sig-meta-analysis [mailto:
> r-sig-meta-analysis-bounces using r-project.org] On Behalf Of Moritz Tobiasch
> Sent: Tuesday, 22 May, 2018 23:01
> To: r-sig-meta-analysis using r-project.org
> Subject: [R-meta] meta-regression scatterplot in ggplot2: code
>
> Dear metafor community,
>
> I recently had the very honour to dig through R code in order to set up a
> meta-regression scatterplot in ggplot2. As this experience was …
> interesting for me, but doesn’t warrant to be repeated by anyone else, I
> allow myself to send my approach to this honorable mailing list, for
> further use as deemed appropriate. @Wolfgang Viechtbauer: of course you may
> add this code (if it seems worth it) to your code examples on
> www.metafor-project.com.
>
> Calculations are closely based on and expand the example of a
> meta-analytic scatterplot as shown on the website
> http://www.metafor-project.org/doku.php/plots:meta_analytic_scatterplot
>
> In order to gain access to all necessary parameters, confidence interval
> boundaries are extracted from the escalc() function by
> plot.dat <- summary.escalc(dat)
> which generates a data.table() with effect size yi, variance vi, standard
> error and confidence interval boundaries ci.lb and ci.ub.
>
> The data can then be put in the ggplot() syntax as following:
>
> ggplot(plot.dat, aes(ablat, exp(yi)))
> + geom_point(pch = 19, cex = 1.5 * sizex) # as, to my experience, ggplot()
> will render dots smaller than the plot() function
> + geom_linerange(aes(ymin = exp(plot.dat$ci.lb), ymax =
> exp(plot.dat$ci.ub)), size = .25) # gives straight lines w/o brackets at
> the ends. if „classical“ look is preferred, use geom_errorbar()
> + scale_y_continuous(trans = log_trans(), limits = c(0.2, 1.6)) # for
> adjustment of axes, see (as example) http://www.cookbook-r.com/Graphs/
> + xlab("Absolute Latitude“)
> + ylab("risk ratio“)
> + geom_hline(yintercept = 1, linetype = "dotted“) # draws the dotted line
> at y = 1 for equal risk ratio
> + geom_line(data = preds, aes(x = preds$ablat, y = preds$pred)) # plots
> the regression line
> + geom_line(data = preds, aes(x = preds$ablat, y = preds$ci.lb), linetype
> = "dashed“) # plots the lower confidence interval boundary
> + geom_line(data = preds, aes(x = preds$ablat, y = preds$ci.ub), linetype
> = "dashed“) # plots the upper confidence interval boundary
>
> Labeling of individual data points was not in the scope of my work, but
> could be done by the geom_text(aes(label = label)) command.
>
> Hope this helps.
>
> Cheers
> Moritz
>
> --
> Dr. med. Moritz Tobiasch
>
> Kirchgasse 22b
> A-6020 Innsbruck
> Austria
>
> Tel.: +43 650 5667954
> moritztobiasch using gmail.com
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