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Re: [Orgmode] graphing from org-tables


From: Eric Schulte
Subject: Re: [Orgmode] graphing from org-tables
Date: Mon, 28 Jul 2008 08:32:22 -0700

Hi Dan,

One way around the sleep(60) hack may be to create the R graph using
an inferior R process.  See
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/address@hidden>-|
 > >  > 
 > >  > 
 > >  > _______________________________________________
 > >  > Emacs-orgmode mailing list
 > >  > Remember: use `Reply All' to send replies to the list.
 > >  > address@hidden
 > >  > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
 > > 
 > > -- 
 > > schulte
 > > 
 > > 
 > > _______________________________________________
 > > Emacs-orgmode mailing list
 > > Remember: use `Reply All' to send replies to the list.
 > > address@hidden
 > > http://lists.gnu.org/mailman/listinfo/emacs-orgmode

-- 
schulte




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