Re: using gnuplot's "splot" and "every" commands on org-mode table data

[Eric Schulte <schulte.eric@gmail.com>]

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Paul Stansell <paulstansell@gmail.com> writes:

> Hello everyone,
>
> I'd be grateful if someone would offer me advice on using gnuplot's
> "splot" and "every" commands when plotting data from a table within
> org-mode.
>
> As far as I can tell, these gnuplot commands do not work properly
> because org-mode exports empty fields in tables as "" and gnuplot's
> "every" and splot commands expect the data file to be formatted as a
> datablock with blank lines marking the boundaries between datablocks.
> (For the definition of a datablock, type "help glossary" at the
> gnuplot prompt.)
>
> I'm using org-mode version 8.0.2 and emacs version 24.2.1 on a
> Fedora-18 system
>
>
> To illustrate my point, consider a blocked datafile called "block.dat"
> containing the following:
>
>   1       1       2
>   1       2       5
>   1       3       10
>
>   2       1       5
>   2       2       8
>   2       3       13
>
>   3       1       10
>   3       2       13
>   3       3       18
>
> For this file the gnuplot command
>
>    #+begin_src gnuplot :var d="block.dat" :results silent
>      plot "$d" u 2:3 ev :::0::0, "" u 2:3 ev :::1::1, "" u 2:3 ev :::2::2
>    #+end_src
>
> shows three separate lines of different colours as gnuplot
> recognises the datafile as blocked data.
>
> Also, the following command produces a surface plot
>
>    #+begin_src gnuplot :var d="block.dat" :results silent
>      splot "$d" u 1:2:3
>    #+end_src
>
> However, if I put the same data in the table below
>
>    #+tblname: data
>    | 1 | 1 |  2 |
>    | 1 | 2 |  5 |
>    | 1 | 3 | 10 |
>    |   |   |    |
>    | 2 | 1 |  5 |
>    | 2 | 2 |  8 |
>    | 2 | 3 | 13 |
>    |   |   |    |
>    | 3 | 1 | 10 |
>    | 3 | 2 | 13 |
>    | 3 | 3 | 18 |
>
> and use the following plot command
>
>    #+begin_src gnuplot :var d=data :results silent
>      plot "$d" u 2:3 ev :::0::0, "" u 2:3 ev :::1::1, "" u 2:3 ev :::2::2
>    #+end_src
>
> the result is a plot of a single line of the same colour as gnuplot
> joins all of the points in the data file.  This seems to be because
> org-mode exports the table as
>
>   "x"     "y"     "z"
>   1       1       2
>   1       2       5
>   1       3       10
>   ""      ""      ""
>   2       1       5
>   2       2       8
>   2       3       13
>   ""      ""      ""
>   3       1       10
>   3       2       13
>   3       3       18
>
> and gnuplot does not recognise this as a blocked data file because it
> contains no blank lines.
>
> The same problem occurs for
>
>    #+begin_src gnuplot :var d=data :results silent
>      splot "$d" u 1:2:3
>    #+end_src
>
> which does not produce a gridded surface plot.
>
> Thanks for your help,
>

Hi Paul,

While I can't claim to fully follow your gnuplot examples, i would
recommend using an intervening shell code block to parse the Org-mode
table data into something that gnuplot will ingest.

If I understand your use case correctly, then something like the
following should work.


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#+name: data
| 1 | 1 |  2 |
| 1 | 2 |  5 |
| 1 | 3 | 10 |
|   |   |    |
| 2 | 1 |  5 |
| 2 | 2 |  8 |
| 2 | 3 | 13 |
|   |   |    |
| 3 | 1 | 10 |
| 3 | 2 | 13 |
| 3 | 3 | 18 |

#+name: clean
#+begin_src sh :var data=data :results file :file /tmp/data.gnuplot
  echo "$data" > /tmp/data.gnuplot
#+end_src

#+begin_src gnuplot :var data=clean(data) :results silent
  splot "$data" u 1:2:3
#+end_src

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If you really wanted to be fancy, gnuplot will let you specify shell
transformations as part of the plotting command which would allow you to
forego the intermediate code block.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte