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From: Dan Davison <davison@stats.ox.ac.uk>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: Org-mode <emacs-orgmode@gnu.org>
Subject: Re: graphing from org-tables
Date: Sat, 26 Jul 2008 19:15:24 +0100	[thread overview]
Message-ID: <20080726181524.GA10786@stats.ox.ac.uk> (raw)
In-Reply-To: <488a2450.1e078e0a.2bc0.181f@mx.google.com>

R (www.r-project.org) is pretty good for data plotting and statistical
analyses. Here's my effort at the org-table-plot function, using
R. Since R contains a csv importer that can read from stdin, it's
pretty simple. I've tried to code it so that you can provide an
arbitrary R function as the optional argument, so in principle you can
do to your org-table anything that R is capable of in the realms of
data analysis and visualisation.

(defun org-table-R-plot (&optional R-function)
"Plot the current table using R. The table is transformed into a dataframe in R. Optional
argument R-function is a string which is either the name of an R
function, or an anonymous function definition of the form (function(d) {...}),
requiring a single argument (the dataframe). The default is to use
the R function 'plot' which produces scatter plots of all pairwise
combinations of columns. An example custom plotting function is:
* plot column 3 against column 1, adding least-squares linear regression fit in blue                                                                                                                               (function(df) { plot(x=df[,1], y=df[,3]) ; abline(lm(df[,3] ~ df[,1]), col=\"blue\") })                                                                                                                      "
  (interactive)
  (unless R-function (set 'R-function "plot"))
  (let ((file (make-temp-file "org-table-R-plot")))
    (org-table-export file "orgtbl-to-csv")
    (set-buffer (find-file-noselect file))
    (shell-command-on-region
     (point-min) (point-max)
     (concat "Rscript -e 'X11() ; " R-function "(read.csv(\"stdin\")) ; system(\"sleep 60\")'"))
    (delete-file file)))


R is at www.r-project.org 
(package r-base on ubuntu/debian)

Rscript is a command line non-interactive scripting utility that is
bundled automatically with the R installation. I reckon it'll be OK on
OSX but no idea about Windows.  My function doesn't have to be used
for plotting; the R-function argument can be any function operating on
the data from the org-table, producing numerical or graphical output.

There's several things that need to be sorted out with my function, e.g.

(i) I haven't worked out how to return control to the emacs process
while keeping the plot window there. I tried adding an & to the
shell-command, but that seemed to result in R receiving nothing on
stdin. So I've got that 'sleep 60' hack in there currently; use C-g if
you get bored of your plot.

(ii) If the R-function isn't doing graphics, then the call to X11()
gets in the way. X11() would only work on linux/mac OSX(?) anyway.

(iii) I'm afraid I don't even know yet how to pass the optional string
argument using M-x org-table-R-plot. Is it possible with some sort of
prefix argument, and an (interactive something) declaration? Anyway,
it seems to work if you evaluate e.g.

(org-table-R-plot "(function(df) { plot(x=df[,1], y=df[,3]) ; abline(lm(df[,3] ~ df[,1]), col=\"blue\") })")

Suggestions for improvements welcome!

Dan



On Fri, Jul 25, 2008 at 12:07:00PM -0700, Eric Schulte wrote:
> 
> I had some time waiting for things to execute, so I condensed your
> process into a single command (borrowing heavily from
> org-export-table).
> 
> (defun org-table/gnuplot (&optional x-col)
>   "Plot the current table using gnuplot.  Use a prefix argument
> to specify a column to use for the x-coordinates, to use the row
> number for the x-coordinates provide a prefix argument of 0."
>   (interactive "p")
>   (message (format "%S" x-col))
>   (unless (org-at-table-p)
>     (error "No table at point"))
>   (require 'org-exp)
>   (require 'gnuplot)
>   (org-table-align) ;; make sure we have everything we need
>   (let* ((beg (org-table-begin))
> 	 (end (org-table-end))
> 	 (cols (save-excursion
> 		 (goto-char end)
> 		 (backward-char 3)
> 		 (org-table-current-column)))
> 	 (data-beg (if (and 
> 			(goto-char beg)
> 			(re-search-forward org-table-dataline-regexp end t)
> 			(re-search-forward org-table-hline-regexp end t)
> 			(re-search-forward org-table-dataline-regexp end t))
> 		       (match-beginning 0)
> 		     beg))
> 	 (skip (- (line-number-at-pos data-beg) (line-number-at-pos beg)))
> 	 (exp-format (format "orgtbl-to-tsv :skip %d" skip))
> 	 (file (make-temp-file "org-table-plot")))
>     ;; export table
>     (org-table-export file exp-format)
>     (with-temp-buffer
>       ;; write script
>       (insert (org-table/gnuplot-script file x-col cols))
>       ;; graph table
>       (gnuplot-mode)
>       (gnuplot-send-buffer-to-gnuplot)
>       (bury-buffer (get-buffer "*gnuplot*")))
>     (delete-file file)))
> 
> (defun org-table/gnuplot-script (file x-col num-cols)
>   (let ((plot-str "'%s' using %s:%d with lines title '%d'");; "\\\n    ,"
> 	script)
>     (dotimes (col (+ 1 num-cols))
>       (unless (or (and x-col (equal col x-col)) (equal col 0))
> 	(setf script (cons (format plot-str file (or (and x-col (format "%d" x-col)) "") col col) script))))
>     (concat "plot " (mapconcat 'identity (reverse script) "\\\n    ,"))))
> 
> On Friday, July 25, at 17:25, James TD Smith wrote:
>  > On 2008-07-25 08:53:31(-0700), Eric Schulte wrote:
>  > > 
>  > > Any advice for quick graphing of a table in org-mode?
>  > > 
>  > 
>  > I have a setup for plotting data from tables. I'm not sure if it's exactly what
>  > you want, but yoy may find it useful.
>  > 
>  > 1. Add the following to your .emacs:
>  > 
>  > (defun ahkt-plot-table (script)
>  >   "util function to export and plot a table using the supplied
>  > gnuplot `script'"
>  >   (org-table-export)
>  >   (let ((cbuf (current-buffer))
>  > 	(cwin (selected-window)))
>  >     (save-restriction
>  >       (save-excursion
>  > 	(find-file script)
>  > 	(gnuplot-send-buffer-to-gnuplot)
>  > 	(bury-buffer)
>  > 	(bury-buffer (get-buffer "*gnuplot*"))))
>  >     (and (window-live-p cwin) (select-window cwin))
>  >     (switch-to-buffer cbuf)
>  >     (delete-other-windows)))
>  > 
>  > 2. Create a gnuplot script which plots data from a file.
>  > 
>  > 3. Add the following properties to the headline containing the table.
>  > TABLE_EXPORT_FILE <filename in the gnuploy script>
>  > TABLE_EXPORT_FORMAT orgtbl-to-generic :skip 4 :splice t :sep "\t"
>  > 
>  > 4. Add an org link in the table (it must be in the table otherwise the export
>  > doesn't work) as below:
>  > [[elisp:(ahkt-plot-table "<gnuplot script>")][plot table]] 
>  > 
>  > I suggest you put it at the top of the table.
>  > You will then need to adjust the 'skip' parameter in the export format depending
>  > on the number of lines at the top of the table which should not be exported
>  > (hlines, more than one plotting link etc). 
>  > 
>  > 5. You should then be able to open the link, and get a plot of the table
>  > contents.
>  > 
>  > 
>  > --
>  > |-<James TD Smith>-<email/ahktenzero@mohorovi.cc>-|
>  > 
>  > 
>  > _______________________________________________
>  > Emacs-orgmode mailing list
>  > Remember: use `Reply All' to send replies to the list.
>  > Emacs-orgmode@gnu.org
>  > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> 
> -- 
> schulte
> 
> 
> _______________________________________________
> Emacs-orgmode mailing list
> Remember: use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

  reply	other threads:[~2008-07-26 18:15 UTC|newest]

Thread overview: 19+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2008-07-25 15:53 graphing from org-tables Eric Schulte
2008-07-25 16:23 ` Carsten Dominik
2008-07-25 16:25 ` James TD Smith
2008-07-25 16:33   ` Carsten Dominik
2008-07-25 17:14   ` Eric Schulte
2008-07-25 19:07   ` Eric Schulte
2008-07-26 18:15     ` Dan Davison [this message]
2008-07-28 15:32       ` Eric Schulte
2008-07-28 15:41         ` Dan Davison
2008-12-21 20:31           ` Dan Davison
2008-12-22 17:00             ` Eric Schulte
2009-01-22 16:27               ` Dan Davison
2009-01-23  1:37                 ` Eric Schulte
2009-01-23  7:30                   ` Carsten Dominik
2009-01-26  8:53                     ` Carsten Dominik
2009-01-28  3:06                       ` Dan Davison
2009-01-28 10:18                         ` Carsten Dominik
     [not found]     ` <C8C13077-8B16-4E8C-8425-5782CE1EDC98@uva.nl>
     [not found]       ` <488b7c9b.14be600a.11cc.ffff9150@mx.google.com>
     [not found]         ` <9629760B-7606-42FD-B625-FAC44490221C@uva.nl>
2008-07-28 14:26           ` Eric Schulte
2008-07-28 21:00             ` Carsten Dominik

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