Re: graphing from org-tables

[Dan Davison <davison@stats.ox.ac.uk>]

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
>  > > 
>  > > 
>  > > _______________________________________________
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> 
> -- 
> schulte