[R] Graphs for scientific publication ?

Bert Gunter gunter.berton at gene.com
Thu Apr 30 20:41:17 CEST 2015


I suggest you have a look at the latest edition of Paul Murrell's
book, "R Graphics", as you seem to be unaware that ggplot2 (as well as
a 3rd graphics paradigm, the lattice package) and base graphics are
built on 2 different and incompatible graphics engines.

Obviously, you are entitled to your opinions and graphical
predilections vary, but I do not think R-Help is a good venue for
these sorts of discussions. The R-devel list might be a better place
to discuss such matters.


Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll

On Thu, Apr 30, 2015 at 5:05 AM, Jeremy Clark <jeremyclarkbio at gmail.com> wrote:
> Dear All,
> First of all, many thanks to all R contributors for a fantastic
> program, and especially to Hadley Wickham for creating ggplot2. The
> following is intended to be a warning that, if the apparently
> superficial problems described are not sorted out, R could well find
> itself being superceded. The reason is that a new user wants to draw a
> graph, and perhaps publish in a scientific journal a graph created
> using R, well before wanting to do a complex regression (and the
> latter is relatively easy). So here goes:
> 1) The saga of the straight line. I implemented a geom_abline - it
> looked superb. Unfortunately I had to disable clip to allow text - now
> my abline looked ridiculous. My search found plotrix: ablineclip -
> fantastic I thought - but it applies to plot and not geom_plot. I
> switched to geom_segment - the rendering looked trash. I switched to
> geom_smooth - should work but as I don't know the x values beforehand
> I'll have to clip a new dataframe - it that a hassle ? - Yes it is !
>             So my general question is - why isn't ggplot2 already part
> of R base - or at least if someone is to create useful packages for
> plot - perhaps a subtle hint could be made that they should also apply
> to ggplot2 (and perhaps to lattice ?? - also personally I would scrap
> qplot as an unnecessary distraction which is not easier to implement
> than ggplot). In general duplication of packages for plot and ggplot
> doesn't seem like a good idea.
> 2) The saga of the italic letter. I found, to my dismay, that to
> insert an italic letter into my plot I had to learn a whole new
> language called plotmath - which wouldn't accept normal R coding, and
> didn't even have normal control functions such as /n for a new line.
> This is ridiculous (and I'm not sure how plotmath managed to get into
> R base).
>             So my question is, when is plotmath going to have a
> complete overhaul to allow eg. "," instead of, or as well as, ~,~, and
> normal control functions such as \n ?
> 3) A related question to (2) is: where is geom_textbox ?
> 4) Where are examples with scientific graph defaults ?  (meaning a
> two-axis graph which is publishable - I will post my own after this is
> published in a years time, but as suggested above, while the graph
> looks good the implementation of this is not pretty).
> Having said that - good luck with implementation - and many thanks for
> all your hard work !
> Yours sincerely,
> Abiologist
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