Hello,
This is an FYI for those using org-babel-R with grid-based graphical
systems.
The documentation for org-babel-R says, "If a :file filename.ext header
arg is provided to an R block, then graphical output from the source
block is captured on disk, and the output of the source block is a link
to the resulting file".
This is true for traditional R graphics, but needs a modifier for
grid-based R graphics, e.g., the lattice and ggplot2 packages.
The graphics functions from lattice and ggplot2 return objects that must
be explicitly printed to see them, using the print function. This
happens automatically when run interactively, e.g. :session, but when
called inside another function, it does not. The way :results value is
defined to operate, my device and ggplot2 function calls are wrapped in
a 'main' function, and unless I specifically print the object, no output
is produced.
Another solution is to use :results output in those source headers that
produce graphical output from these packages.
I believe the following org-mode file summarizes the different ways of
getting this working.
============= org-mode code begins ==================
* Note that my .Rprofile loads the lattice package, i.e., library(lattice)
* does /not/ produce a file
#+begin_src R :file 1.png :results value
xyplot(1:10 ~ 1:10)
#+end_src
* does produce a file, by printing object
#+begin_src R :file 2.png :results value
print(xyplot(1:10 ~ 1:10))
#+end_src
* does produce a file, by using :results output
#+begin_src R :file 3.png :results output
xyplot(1:10 ~ 1:10)
#+end_src
* does produce a file, by evaluating in :session
#+begin_src R :file 4.png :session
xyplot(1:10 ~ 1:10)
#+end_src
========= end org-mode code ========================
The following R code shows something potentially interesting
=========== begin R code ==============================
## this produces a graphic when run with R CMD BATCH
myfun <- function() {
xyplot(1:10 ~ 1:10)
}
png("with-function-wrapper-outside.png")
myfun()
dev.off()
## this does not produce a graphic with R CMD BATCH
myfun <- function() {
png("with-function-wrapper-inside.png")
xyplot(1:10 ~ 1:10)
dev.off()
}
myfun()
============== End R code =============================
In effect, :results value is doing the latter of the two things in the R
code above. If the process were reversed, i.e., the 'main' function
call was wrapped in the graphics function, as in example 1 above, I
believe it would work. Of course, this isn't how it is currently
implemented, and may introduce other complexities. There are also
solutions as I've posted above.
--Erik
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