[R] Graphs for scientific publication ?

Jeremy Clark jeremyclarkbio at gmail.com
Thu Apr 30 14:05:55 CEST 2015

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itself being superceded.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,


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