* Trying to use :post header argument to set #+ATTR_LATEX: line
@ 2018-10-22 14:43 L.C. Karssen
2018-10-22 16:42 ` Berry, Charles
0 siblings, 1 reply; 3+ messages in thread
From: L.C. Karssen @ 2018-10-22 14:43 UTC (permalink / raw)
To: Org Mode
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Dear list,
I'd like to create several tables from R and export those to a LaTeX
document. Because only input variable differs for the R code that
generates the tables, I thought I could use the :post header argument to
add the #+ATTR_LATEX: line I need to each of the outputs of my R source
code blocks.
I tried to follow the Org manual (section 14.8.2.27), but that doesn't
seem to work. My R results blocks all get colons in front of the output
and if I set :results drawer, I get the following error:
org-babel-R-evaluate-session: Wrong type argument: listp,
followed by a double quoted string containing the data, excluding the
#+ATTR_LATEX line.
I have attached an example Org file that illustrates what I am trying to
achieve and where it goes wrong. I tested this using Emacs 26.1 of
2018-05-29 and Org 9.1.13 from elpa (2018-06-25).
In short, I'm trying the following:
#+name: attr_wrap
#+begin_src R :var data="" :results output
cat("#+ATTR_LATEX: :environment tabularx :width \\textwidth :align
Xrrr", "\n")
data
#+end_src
#+name: create_table2
#+begin_src R :rownames yes :colnames yes :var brand="Mazda" :post
attr_wrap(data=*this*)
mtcars[grepl(brand, rownames(mtcars)), c("mpg", "cyl", "disp")]
#+end_src
And call it:
#+call: create_table2(brand="Toyota")
#+RESULTS:
: #+ATTR_LATEX: :environment tabularx :width \textwidth :align Xrrr
: X mpg cyl disp
: 1 Toyota Corolla 33.9 4 71.1
: 2 Toyota Corona 21.5 4 120.1
Note that the whole results block is preceded by a colon, instead
of the table being formatted by Org.
Thanks for any help!
Best regards,
Lennart.
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
's-Hertogenbosch
The Netherlands
lennart@karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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#+TITLE: Testing the :post header arg
# Set some Org Babel values for the whole document
#+PROPERTY: header-args:R :session *myR*
* Introduction
In this document I explore the use of the =:post= header argument
for Org mode source code blocks. My aim is to create several tables
for export to LaTeX and have the =ATTR_LATEX= blocks automatically
added to the output of the source code blocks.
For these tests we wil use the =mtcars= data set that comes with R.
* Testing the =:post= header argument
The following block is supposed to be used in a =:post= call to set
the =ATTR_LATEX= line.
#+name: attr_wrap
#+begin_src R :var data="" :results output
cat("#+ATTR_LATEX: :environment tabularx :width \\textwidth :align Xrrr", "\n")
data
#+end_src
The idea is to use this as a named src block so it can be reused for
each table I want to create (here still without =:post= to show the
regular output).
#+name: create_table
#+begin_src R :rownames yes :colnames yes :var brand="Mazda"
mtcars[grepl(brand, rownames(mtcars)), c("mpg", "cyl", "disp")]
#+end_src
This works using =#+call:=:
#+call: create_table(brand="Hornet")
#+RESULTS:
| | mpg | cyl | disp |
|-------------------+------+-----+------|
| Hornet 4 Drive | 21.4 | 6 | 258 |
| Hornet Sportabout | 18.7 | 8 | 360 |
Define a slightly different src block that actually uses the =:post=
header argument:
#+name: create_table2
#+begin_src R :rownames yes :colnames yes :var brand="Mazda" :post attr_wrap(data=*this*)
mtcars[grepl(brand, rownames(mtcars)), c("mpg", "cyl", "disp")]
#+end_src
And call it:
#+call: create_table2(brand="Toyota")
#+RESULTS:
: #+ATTR_LATEX: :environment tabularx :width \textwidth :align Xrrr
: X mpg cyl disp
: 1 Toyota Corolla 33.9 4 71.1
: 2 Toyota Corona 21.5 4 120.1
Note that the whole results block is preceded by a colon, instead
of being formatted by Org.
Using the Shell code from the Org manual doesn't work either, it
adds a comma in front of the =#+ATTR_LATEX= line.
#+name: attr_wrap2
#+begin_src sh :var data="" :results output
echo "#+ATTR_LATEX: :environment tabularx :width \\textwidth :align Xrrr"
echo "$data"
#+end_src
New =create_table= function:
#+name: create_table3
#+begin_src R :rownames yes :colnames yes :var brand="Mazda" :post attr_wrap2(data=*this*)
mtcars[grepl(brand, rownames(mtcars)), c("mpg", "cyl", "disp")]
#+end_src
And call it:
#+call: create_table3(brand="Toyota")
#+RESULTS:
: #+ATTR_LATEX: :environment tabularx :width \textwidth :align Xrrr
: Toyota Corolla 33.9 4 71.1
: Toyota Corona 21.5 4 120.1
Observe that now the column names have completely disappeared.
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^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Trying to use :post header argument to set #+ATTR_LATEX: line
2018-10-22 14:43 Trying to use :post header argument to set #+ATTR_LATEX: line L.C. Karssen
@ 2018-10-22 16:42 ` Berry, Charles
2018-10-23 20:12 ` L.C. Karssen
0 siblings, 1 reply; 3+ messages in thread
From: Berry, Charles @ 2018-10-22 16:42 UTC (permalink / raw)
To: L.C. Karssen; +Cc: Org Mode
> On Oct 22, 2018, at 7:43 AM, L.C. Karssen <lennart@karssen.org> wrote:
>
> Dear list,
>
> I'd like to create several tables from R and export those to a LaTeX
> document. Because only input variable differs for the R code that
> generates the tables, I thought I could use the :post header argument to
> add the #+ATTR_LATEX: line I need to each of the outputs of my R source
> code blocks.
>
> I tried to follow the Org manual (section 14.8.2.27), but that doesn't
> seem to work. My R results blocks all get colons in front of the output
> and if I set :results drawer, I get the following error:
I do not doubt that this is possible with enough tooling. I think it will be easier with the xtable R package.
But for issues like this I usually find it easier to export the document to *.Rmd (R markdown) or *.Rnw (knitr) and render from there.
See https://github.com/chasberry/orgmode-accessories for some examples.
HTH,
Chuck
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Trying to use :post header argument to set #+ATTR_LATEX: line
2018-10-22 16:42 ` Berry, Charles
@ 2018-10-23 20:12 ` L.C. Karssen
0 siblings, 0 replies; 3+ messages in thread
From: L.C. Karssen @ 2018-10-23 20:12 UTC (permalink / raw)
To: Berry, Charles; +Cc: Org Mode
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Dear Chuck,
Thanks for suggesting xtables. I have used it in the past, but had more
or less forgotten about it. I'll give it a try again.
Best regards,
Lennart.
On 22-10-18 18:42, Berry, Charles wrote:
>
>
>> On Oct 22, 2018, at 7:43 AM, L.C. Karssen <lennart@karssen.org> wrote:
>>
>> Dear list,
>>
>> I'd like to create several tables from R and export those to a LaTeX
>> document. Because only input variable differs for the R code that
>> generates the tables, I thought I could use the :post header argument to
>> add the #+ATTR_LATEX: line I need to each of the outputs of my R source
>> code blocks.
>>
>> I tried to follow the Org manual (section 14.8.2.27), but that doesn't
>> seem to work. My R results blocks all get colons in front of the output
>> and if I set :results drawer, I get the following error:
>
> I do not doubt that this is possible with enough tooling. I think it will be easier with the xtable R package.
>
> But for issues like this I usually find it easier to export the document to *.Rmd (R markdown) or *.Rnw (knitr) and render from there.
>
> See https://github.com/chasberry/orgmode-accessories for some examples.
>
>
> HTH,
>
> Chuck
>
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
's-Hertogenbosch
The Netherlands
lennart@karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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^ permalink raw reply [flat|nested] 3+ messages in thread
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2018-10-22 14:43 Trying to use :post header argument to set #+ATTR_LATEX: line L.C. Karssen
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