Hi all,
Andreas Leha <andreas.l...@med.uni-goettingen.de> writes:
> Hi Chuck,
>
> "Charles C. Berry" <ccbe...@ucsd.edu> writes:
>> On Mon, 14 Dec 2015, Andreas Leha wrote:
>>
>>> Hi all,
>>>
>>> I'd like to hear your ideas on how to include noweb references to code
>>> blocks in a way that the default values are used as parameter values.
>>>
>>> Here is a little example:
>>>
>>> #+PROPERTY: header-args:R :session *testR*
>>>
>>> The background is that I like to use Org mode table to record small data.
>>>
>>> #+name: datatable
>>> | A | B |
>>> |---+----|
>>> | 1 | 10 |
>>> | 2 | 20 |
>>>
>>> Usually I want to pre-process and/or convert such data.
>>>
>>> #+name: read_datatable
>>> #+header: :var datatable=datatable
>>> #+begin_src R :results none
>>> datatable$B <- 10 * datatable$B
>>> #+end_src
>>>
>>> Later I would like to use that data in larger (R-) code blocks. I'd
>>> like such code blocks to DWIM:
>>>
>>> #+name: some_code
>>> #+begin_src R :noweb yes :results graphics :file testplot.png
>>> <<read_datatable>>
>>> plot(datatable$A, datatable$B)
>>> #+end_src
>>>
>>> But they do not: They are not stand alone and do not execute -- unless I
>>> executed `read_datatable' manually/by chance upfront.
>>
>> Try this:
>>
>> #+name: read_datatable
>> #+header: :var datatable=datatable
>>
>> #+begin_src R :results value :colnames yes
>> datatable$B <- 10 * datatable$B
>> datatable
>> #+end_src
>>
>> #+name: some_code
>> #+HEADER: :var datatable=read_datatable()
>>
>> #+begin_src R :noweb yes :results graphics :file testplot.png
>> plot(datatable$A, datatable$B)
>> #+end_src
>>
>
> Thanks! I am aware of that possibility. Should have posted a more
> involved example. This works if I only return a table. Or something
> else, that can be passed through Org. But it fails for instance if the
> result is a function (or more functions...).
>
In case anyone is interested. I came up with a quite simple code block
that does what I want:
--8<---------------cut here---------------start------------->8---
#+name: org_exec
#+header: :var srcblock=""
#+begin_src emacs-lisp :results silent
(save-excursion
(org-babel-goto-named-src-block srcblock)
(org-babel-execute-src-block)
)
(concat srcblock " executed")
#+end_src
--8<---------------cut here---------------end--------------->8---
Now, I can do
--8<---------------cut here---------------start------------->8---
#+name: some_code
#+begin_src R :session *testR* :noweb yes :results graphics :file testplot.png
<<org_exec("read_datatable")>>
plot(datatable$A, datatable$B)
#+end_src
--8<---------------cut here---------------end--------------->8---
The remaining downside is that I have to take care of running things in
the correct session.
Best,
Andreas
PS: complete example:
--8<---------------cut here---------------start------------->8---
* Org
#+name: org_exec
#+header: :var srcblock=""
#+begin_src emacs-lisp :results silent
(save-excursion
(org-babel-goto-named-src-block srcblock)
(org-babel-execute-src-block)
)
(concat "\"" srcblock " executed" "\"")
#+end_src
* Data
#+name: datatable
| A | B |
|---+----|
| 1 | 10 |
| 2 | 20 |
#+name: read_datatable
#+header: :var datatable=datatable
#+begin_src R :session *testR* :results value :colnames yes
datatable$B <- 10 * datatable$B
datatable
#+end_src
#+results: read_datatable
| A | B |
|---+-----|
| 1 | 100 |
| 2 | 200 |
* Analysis
#+name: some_code
#+begin_src R :session *testR* :noweb yes :results graphics :file testplot.png
<<org_exec("read_datatable")>>
plot(datatable$A, datatable$B)
#+end_src
#+results: some_code
[[file:testplot.png]]
--8<---------------cut here---------------end--------------->8---
