[R] Graphs for scientific publication ?

[David L Carlson]

More useful to the r-help list would be a reproducible example of the data you are using and a clear statement of what you are trying to accomplish. It is likely that all of your requirements can be easily met, but you spent most of your message talking about what you have tried without telling us where you want to end up. People on the list are familiar with base graphics, lattice graphics, and ggplot2. If you list your requirements clearly, you might end up with three solutions.

-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Bert Gunter
Sent: Thursday, April 30, 2015 1:41 PM
To: Jeremy Clark
Cc: r-help at r-project.org
Subject: Re: [R] Graphs for scientific publication ?

Jeremy:

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.

Cheers,
Bert

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 itself being superceded.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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