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itself being superceded.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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