[Orgmode] gnuplot with errorbars in org-mode

[Suvayu Ali]

Hi everyone,

I am a new org-mode user and this is my first post to the mailing list. 
Lately I have been using org-mode to manage the data for a study I'm 
doing for my research project. I primarily use the spreadsheet features 
to do all the calculations and then use gnuplot to plot the final 
result. For all the basic plotting it works great, but I am having 
trouble when I want error bars in my plot.

To demonstrate my point here is a small example.

> #+PLOT: title:"My plot" ind:1 deps:(2) type:2d with:xyerrorlines
> | Abscissa (X) | Ordinate (Y) | X low edge | X high edge | Y low edge | Y high 
> edge |
> |--------------+--------------+------------+-------------+------------+-------------|
> |           60 |    1.1140741 |       0020 |        0100 |  1.1699508 |   
> 1.0680423 |
> |          150 |    1.1187818 |       0100 |        0200 |  1.1593492 |   
> 1.0855438 |
> |          350 |    1.1193459 |       0200 |        0500 |  1.1331885 |   
> 1.1086636 |
> |          600 |    1.1029173 |       0500 |        0700 |  1.0940769 |   
> 1.1121185 |
> |          850 |    1.0841388 |       0700 |        1000 |  1.0676310 |   
> 1.1000886 |
> |         1250 |    1.0358938 |       1000 |        1500 |  1.0127586 |   
> 1.0586916 |
> |         2000 |   0.89370079 |       1500 |        2500 | 0.88014981 |       
> 0.925 |

This gives me an error like this,

> gnuplot> plot '/tmp/org-plot30213YHV' using 1:2 with xyerrorlines title 
> 'Ordinate (Y)'
>          Not enough columns for this style

I have tried changing the "#+PLOT:" line to say this,

> #+PLOT: title:"My plot" ind:1 deps:(2 3 4 5 6) type:2d with:xyerrorlines

But that doesn't work either. I think the problem is org-plot doesn't 
recognise that when plotting with error bars, gnuplot expects more than 
two columns of data. So a command like this should be sent to gnuplot,

> plot '/tmp/org-plot30213YHV' using 1:2:3:4:5:6 with xyerrorlines title 
> 'Ordinate (Y)'

In fact typing this on the gnuplot terminal actually generates the 
desired plot!


So I thought maybe I should try org-babel. So I tried something like this,

> #+srcname: plot-data-w-err
> #+begin_src gnuplot
>   set title 'My plot'
>   plot 'data-table' using 1:2:3:4:5:6 with xyerrorlines title 'Ordinate (Y)'
> #+end_src

and gave my table a name like this,

#+tblname: data-table

But that didn't behave as I was expecting it to. I think I don't quite 
understand how to pass a table as an input to a source block.

I was hoping someone on the list could either help me understand how 
babel uses tables as inputs, or pass the correct command to gnuplot with 
org-plot. BTW, org-mode is phenomenal. Loving every bit of it. Thank you 
Carsten /et al./ :)

Specifics:
Org-mode version 7.01
GNU Emacs 23.2.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.20.1) of 
2010-05-13 on x86-07.phx2.fedoraproject.org
gnuplot 4.4 patchlevel 0

--
Suvayu

Open source is the future. It sets us free.