* gnuplot with errorbars in org-mode
@ 2010-07-25 4:26 Suvayu Ali
2010-07-25 14:48 ` Eric Schulte
0 siblings, 1 reply; 3+ messages in thread
From: Suvayu Ali @ 2010-07-25 4:26 UTC (permalink / raw)
To: emacs-orgmode
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.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: gnuplot with errorbars in org-mode
2010-07-25 4:26 gnuplot with errorbars in org-mode Suvayu Ali
@ 2010-07-25 14:48 ` Eric Schulte
2010-07-25 16:53 ` suvayu ali
0 siblings, 1 reply; 3+ messages in thread
From: Eric Schulte @ 2010-07-25 14:48 UTC (permalink / raw)
To: Suvayu Ali; +Cc: emacs-orgmode
Hi,
I think you're on the right path using Org-babel, here is an altered
version of your gnuplot code block which should work.
#+srcname: plot-data-w-err
#+begin_src gnuplot :var data=data-table :file example.png
set title 'My plot'
plot "$data" using 1:2:3:4:5:6 with xyerrorlines title 'Ordinate (Y)'
#+end_src
This assumes that you have named your table with a line like
#+tblname: data-table
Notice that the example above uses two "header arguments", the ":var"
header argument specifies that the data from data-table should be saved
into the variable named "data", and the :file header argument specifies
that gnuplot should save the resulting graph to a file named
"exmaple.png" and that a link to that graph should be inserted on
evaluation of the code block. Please see the quick-guide and the manual
for more information on code block syntax and header arguments.
Best -- Eric
Quick Guide:Babel
http://orgmode.org/guide/Working-With-Source-Code.html#Working-With-Source-Code
Manual:Babel
http://orgmode.org/manual/Working-With-Source-Code.html#Working-With-Source-Code
Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:
> 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
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: gnuplot with errorbars in org-mode
2010-07-25 14:48 ` Eric Schulte
@ 2010-07-25 16:53 ` suvayu ali
0 siblings, 0 replies; 3+ messages in thread
From: suvayu ali @ 2010-07-25 16:53 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode
This works like a charm Eric!!
Now with org-babel working I can imagine all sorts of wonderful
possibilities. I can now have common code blocks which are called to
setup the gnuplot terminal depending on the need (say for png or eps
or just regular interactive) for different sets of data or different
output requirements!
Thank you sooo much. :)
On 25 July 2010 07:48, Eric Schulte <schulte.eric@gmail.com> wrote:
> Hi,
>
> I think you're on the right path using Org-babel, here is an altered
> version of your gnuplot code block which should work.
>
> #+srcname: plot-data-w-err
> #+begin_src gnuplot :var data=data-table :file example.png
> set title 'My plot'
> plot "$data" using 1:2:3:4:5:6 with xyerrorlines title 'Ordinate (Y)'
> #+end_src
>
> This assumes that you have named your table with a line like
>
> #+tblname: data-table
>
> Notice that the example above uses two "header arguments", the ":var"
> header argument specifies that the data from data-table should be saved
> into the variable named "data", and the :file header argument specifies
> that gnuplot should save the resulting graph to a file named
> "exmaple.png" and that a link to that graph should be inserted on
> evaluation of the code block. Please see the quick-guide and the manual
> for more information on code block syntax and header arguments.
>
> Best -- Eric
>
> Quick Guide:Babel
> http://orgmode.org/guide/Working-With-Source-Code.html#Working-With-Source-Code
>
> Manual:Babel
> http://orgmode.org/manual/Working-With-Source-Code.html#Working-With-Source-Code
>
> Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:
>
>> 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.
^ permalink raw reply [flat|nested] 3+ messages in thread
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2010-07-25 4:26 gnuplot with errorbars in org-mode Suvayu Ali
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