[R] Graphs for scientific publication ?

Ista Zahn istazahn at gmail.com
Fri May 1 20:06:22 CEST 2015

On Thu, Apr 30, 2015 at 8:05 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 itself being superceded.

In my opinion that can and should happen, but my prediction is that R
has such a big lead in terms of available functionality and packages
that no one will catch up for at least a decade.

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 !

As others have mentioned we can probably help you if you give us a
reproducible example and a clear description of what you are trying to
accomplish. Absent that this just sounds like complaining for the sake
of it.

>             So my general question is - why isn't ggplot2 already part
> of R base

I think packages are added to the base distribution relatively
infrequently these days. Is


really an issue?

- 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 ??

I'm not understanding what you are trying to say here.

- also personally I would scrap
> qplot as an unnecessary distraction which is not easier to implement
> than ggplot).

ggplot2 is in maintenance mode, so it is unlikely that major changes
like that will be introduced.

 In general duplication of packages for plot and ggplot
> doesn't seem like a good idea.

I'm not sure what kind of duplication you are referring to here,
though in general I also wish there was less duplicated functionality
spread across various R packages.

> 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).


d1 <- data.frame(x = 1, y = 1, t = "some text")
d2 <- d1
d2$x <- 2

ggplot(d1, aes(x = x, y = y, label = t)) +
  geom_text(hjust = 0, size = 10) +
  geom_text(data=d2, fontface="italic", hjust=1, size = 10)

Works for me.

>             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 ?

Probably never (though you could do it yourself if you think it is
worth spending the time to improve it).

> 3) A related question to (2) is: where is geom_textbox ?

I don't think there is one. You could make one following the
documentation at

> 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).

Lot's of people publish ggplot2 graphs, standards differ from field to
field and from journal to journal.
will give you some examples. Beyond that I think you'll have to be
more specific about what exactly you want the graphs to look like.

> Having said that - good luck with implementation - and many thanks for
> all your hard work !
> Yours sincerely,
> Abiologist
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