Hi everyone,
should we include Dan's code as a contributed package or
even merge it into org-plot?
- Carsten
On Dec 30, 2008, at 8:35 PM, Dan Davison wrote:
Hi all,
I've had a go at taking the org tables and R thing a bit further. I'm
using two different #+ lines in the org buffer: Lines starting with
#+TBLR: are in the standard org style (option:value) and can be used
to specify certain transformations of the table and standard plots of
the table data. In lines starting #+TBLR:: you can supply literal R
code, giving you full control over what you do with the table. M-x
org-table-R-apply makes happen whatever has been specified in those
lines. As long as the transformation results in something reasonably
one- or two-dimensional, then this is output to the org-buffer as an
org table (you can choose whether or not it replaces the original
table). You need to have R running in an inferior-ess-mode
buffer. Then, if you have this table,
| rowname | col1 | col2 |
|---------+------+------|
| row 1 | 1 | 2 |
| row 2 | 3 | 4 |
| total | | |
#+TBLR:: x[3,] <- x[1,] + x[2,]
#+TBLR: rownames:1
org-table-R-apply turns it into
| rownames(x) | col1 | col2 |
|-------------+------+------|
| row 1 | 1 | 2 |
| row 2 | 3 | 4 |
| total | 4 | 6 |
The action:<something> option specifies off-the-shelf actions, without
having to write any R code. E.g.
| col1 | col2 |
|------+------|
| 1 | 2 |
| 3 | 4 |
#+TBLR: action:transpose
produces
| | V1 | V2 |
|------+----+----|
| col1 | 1 | 3 |
| col2 | 2 | 4 |
and
#+TBLR: action:plot columns:((1)(2)) lines:t rownames:1
would plot column 2 against column 1.
You can mix user-code and off-the-shelf code: in this somewhat
solipsistic example user-supplied code is used to extract the day of
week, and then action:tabulate is used to build a 2-way table:
| author | date |
|---------------------+---------------------------------|
| Carsten Dominik | Thu, 12 Jun 2008 12:51:54 +0200 |
| Carsten Dominik | Wed, 11 Jun 2008 08:57:39 +0200 |
| Adam Spiers | Wed, 11 Jun 2008 12:06:23 +0100 |
| Eddward DeVilla | Wed, 11 Jun 2008 12:15:11 -0500 |
| Eddward DeVilla | Wed, 11 Jun 2008 20:09:50 -0500 |
| Harri Kiiskinen | Wed, 04 Jun 2008 16:38:37 +0200 |
| Carsten Dominik | Thu, 12 Jun 2008 14:15:49 +0200 |
| Harri Kiiskinen | Thu, 12 Jun 2008 14:31:49 +0200 |
| Carsten Dominik | Thu, 12 Jun 2008 16:17:59 +0200 |
| Manoj Srivastava | Mon, 09 Jun 2008 01:52:03 -0500 |
| Daniel Clemente | Wed, 04 Jun 2008 16:35:01 +0200 |
| Carsten Dominik | Mon, 9 Jun 2008 09:56:09 +0200 |
| Carsten Dominik | Tue, 10 Jun 2008 10:05:24 +0200 |
| Adam Spiers | Tue, 10 Jun 2008 10:57:52 +0100 |
| Manuel Hermenegildo | Tue, 10 Jun 2008 13:50:44 +0200 |
| Christian Egli | Tue, 24 Jun 2008 13:27:05 +0200 |
#+TBLR: columns:(1 2) action:tabulate
#+TBLR:: x[,2] <- substr(x[,2], 1, 3)
results in
| | Mon | Thu | Tue | Wed |
|---------------------+-----+-----+-----+-----|
| Adam Spiers | 0 | 0 | 1 | 1 |
| Carsten Dominik | 1 | 3 | 1 | 1 |
| Christian Egli | 0 | 0 | 1 | 0 |
| Daniel Clemente | 0 | 0 | 0 | 1 |
| Eddward DeVilla | 0 | 0 | 0 | 2 |
| Harri Kiiskinen | 0 | 1 | 0 | 1 |
| Manoj Srivastava | 1 | 0 | 0 | 0 |
| Manuel Hermenegildo | 0 | 0 | 1 | 0 |
#+TBLR: action:barplot rownames:1 columns:(1 2 3 4) showcode:t
The #+TBLR: line below that produces a bar plot of the data.
There are more details below. The code is at
http://www.stats.ox.ac.uk/~davison/software/org-table-R/org-table-R.el
It would be great to get any feedback on this. My thought was that
something like this has the potential to provide a unified plotting
and table formula interface, which might be attractive to people who
know and/or like and/or want to learn R. There's lots more that could
be done with this, and there must be all sorts of bugs in it at this
stage. But if there's any interest in it then it could be
improved. Anyway, read on if you're interested in hearing more details
about the options and actions available.
Dan
Currently, the available actions are
- plot
A simple plot of the x and y values. If no x-values are specified
then the the y values are plotted against 1,2,...,length(y). If
lines:t then the points are joined by lines.
- lines
Equivalent to action:plot lines:t
- points
Equivalent to action:plot lines:nil
- barplot
Create a bar plot. A vertical bar is drawn for each row, with
height given by the value in that row. If multiple columns are
selected the bars for different columns are placed side-by-side.
- hist
A histogram
- density
A smoothed histogram
- image
A plot of a table in which each cell is coloured according its
numeric value.
- tabulate
Create a table containing counts of the distinct values of the
columns selected (if v columns are selected, the table will be
v-dimensional, giving the counts of joint occurrences of the
different values of the columns).
- transpose
Transpose the table
. Apart from tabulate and transpose, those produce plots of the
selected columns using the R function of the same name (type
e.g. ?barplot at the R prompt to see the help page).
In addition to the action: option, the following options can be given
on the #+TBLR: line:
- showcode:t
org-table-R-apply creates an R function which hopefully implements
the requested actions (explicit user-supplied code comes first;
off-the-shelf afterwards). With this option that function
definition is displayed in a new R-mode buffer. That could serve as
a starting point for fine-tuning the behaviour. One option would be
to edit that function definition (say you call it f), save it in a
file, and then use
#+TBLR:: source("/path/to/file.R") ; f(x)
- rownames:<integer>
Specifies that column n contains the names of the rows of the
table. These must be unique.
- replace:t
The original org-table is replaced by the text output (which will be
an org-table if the result is like a 1- or 2-dimensional array).
- columns:<lisp-list>
This specifies the columns that the off-the-shelf action will
operate on (e.g. the columns you want to plot). The simplest case
is columns:j, where j is an integer. This could also be written
columns:(j). columns:((1)(2 3)) says that you want a graphic in
which columns 2 and 3 are plotted on the y-axis, and column 1 is
plotted on the x-axis. What form that will take depends on the
plotting function used (action:<something>). It might involve
multiple plots in a single figure, although to be fair I haven't
implemented most of the multiple column options so you're likely to
get an error with anything except for
action:<plot/lines/points>. I've given a description of how columns
are specified, and what sort of behaviour might be expected, in the
docstring to org-table-R-make-index-vectors. Basically, my
intention was that columns:((1)(2 3)) should correspond to
xy.coords(x=1, y=c(2,3)) in R. (See ?xy.coords if you want to get
involved in this.)
- lines:t
When action:plot is given, this means that the points are joined
with lines. That's the same behaviour as action:lines.
- output-to-buffer:t
This specifies that the text output from R goes into the org
buffer. You shouldn't normally need to use this option as the code
tries to work out whether it's appropriate. The rule it follows is
that the org buffer gets the output if any bespoke code has been
supplied on the #+TBLR:: line, or if an action: has been requested
that results in text (action:<tabulate/transpose> at the moment).
p.s.
I agree with Eric that we could do with a way of referencing tables
from remote areas of an org file.
--
http://www.stats.ox.ac.uk/~davison
_______________________________________________
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
_______________________________________________
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
