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: Mon, 28 Jul 2008 16:41:52 +0100 [thread overview]
Message-ID: <20080728154152.GD21509@stats.ox.ac.uk> (raw)
In-Reply-To: <488de67a.1abd600a.16a2.09e7@mx.google.com>
On Mon, Jul 28, 2008 at 08:32:22AM -0700, Eric Schulte wrote:
> Hi Dan,
>
> One way around the sleep(60) hack may be to create the R graph using
> an inferior R process. See
Yep, I just this minute asked for help on the Emacs Speaks Statistics
(ESS) mailing list! I'll report back if I make progress with that.
https://stat.ethz.ch/pipermail/ess-help/2008-July/004785.html
Dan
> http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-and-Emacs for
> information on running R functions from inside of Emacs.
>
> Best -- Eric
>
> On Saturday, July 26, at 19:15, Dan Davison wrote:
> > 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
>
> --
> schulte
next prev parent reply other threads:[~2008-07-28 15:41 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
2008-07-28 15:32 ` Eric Schulte
2008-07-28 15:41 ` Dan Davison [this message]
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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