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+;;; org-R.el --- Numerical computation and data visualisation for org-mode using R
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+
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+;; Copyright (C) 2009
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+;; Free Software Foundation, Inc.
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+
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+;; Author: Dan Davison <davison@stats.ox.ac.uk>
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+;; Keywords: org, R, ESS, tables, graphics
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+;; Homepage: http://www.stats.ox.ac.uk/~davison/software/org-R
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+;; Version: 0.05 2009-02-05
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+;;
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+;; This file is not part of GNU Emacs.
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+;;
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+;; This file is free software; you can redistribute it and/or modify
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+;; it under the terms of the GNU General Public License as published by
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+;; the Free Software Foundation; either version 3, or (at your option)
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+;; any later version.
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+
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+;; This file is distributed in the hope that it will be useful,
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+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+;; GNU General Public License for more details.
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+
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+;; You should have received a copy of the GNU General Public License
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+;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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+;;
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+;;; Commentary:
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+
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+;; This file allows R (http://www.r-project.org) code to be applied to
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+;; emacs org-mode (http://orgmode.org) tables. When the
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+;; result of the analysis is a vector or matrix, it is output back
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+;; into the org-mode buffer as a new org table. Alternatively the R
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+;; code may be used to plot the data in the org table. It requires R to be
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+;; running in an inferior-ess-mode buffer (install Emacs Speaks
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+;; Statistics http://ess.r-project.org and issue M-x R).
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+;;
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+;;
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+;; The user interface is via two different options lines in the org
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+;; buffer. As is conventional in org-mode, these are lines starting
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+;; with `#+'. Lines starting with #+R: specify options in the
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+;; standard org style (option:value) and are used to specify certain
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+;; off-the-shelf transformations and plots of the table data. The
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+;; #+R: line is also used to specify the data to be analysed
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+;; (either an org table or a csv file), and to restrict the analysis
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+;; to certain columns etc. In lines starting #+RR: you can supply
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+;; literal R code, giving you full control over what you do with the
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+;; table. With point in the first #+R line, M-x org-R-apply
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+;; makes happen whatever has been specified in those lines.
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+
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+;; The best documentation is currently the Worg tutorial:
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+;;
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+;; http://orgmode.org/worg/org-tutorials/org-R/org-R.php
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+
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+
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+(defconst org-R-skeleton-funcall-1-arg
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+ "%s(x[%s]%s)"
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+ "Skeleton of a call to an R function.
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+E.g. barplot(x[,3:5], names.arg=rownames(x))")
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+
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+(defconst org-R-skeleton-funcall-2-args
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+ "%s(x[,%s], x[,%s]%s)"
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+ "Skeleton of a call to an R function which can take x and y
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+ args.")
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+
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+(defconst org-R-write-org-table-def
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+ "write.org.table <- function (x, write.rownames = TRUE)
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+{
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+ if(!is.null(dim(x)) && length(dim(x)) > 2)
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+ stop(\"Object must be 1- or 2-dimensional\") ;
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+ if(is.vector(x) || is.table(x) || is.factor(x) || is.array(x))
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+ x <- as.matrix(x) ;
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+ if(!(is.matrix(x) || inherits(x, c('matrix', 'data.frame')))) {
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+ invisible() ;
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+ print(x) ;
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+ stop(\"Object not recognised as 1- or 2-dimensional\") ;
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+ } ;
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+ if(is.null(colnames(x)))
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+ colnames(x) <- rep('', ncol(x)) ;
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+ if(write.rownames)
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+ x <- cbind(rownames(x), x) ;
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+ cat('|', paste(colnames(x), collapse = ' | '), '|\\n') ;
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+ cat('|', paste(rep('----', ncol(x)), collapse = '+'), '|\\n', sep = '') ;
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+ invisible(apply(x, 1, function(row) cat('|', paste(row, collapse = ' | '), '|\\n'))) ;
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+}"
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+ "Definition of R function to write org table representation of R objects.
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+To see a more human-readable version of this, look at the code,
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+or type dput(write.org.table) RET at the R (inferior-ess-mode
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+buffer) prompt.")
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+
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+
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+(defun org-R-apply ()
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+ "Construct and evaluate an R function call.
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+Construct an R function corresponding to the #+R: and #+RR:
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+lines. R must be currently running in an inferior-ess-mode
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+buffer. The function evaluates any user-supplied R code in the
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+#+RR: line before the off-the-shelf actions specified in the #+R:
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+line. The user-supplied R code can operate on a variable called x
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+that is the org table represented as a data frame in R. Text
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+output from the R process may be inserted into the org buffer, as
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+an org table where appropriate."
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+ (interactive)
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+ (require 'ess)
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+ (save-excursion
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+ (beginning-of-line)
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+ (unless (looking-at "#\\+RR?:") (error "Point must be in a #+R or #+RR line"))
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+ (while (looking-at "#\\+RR?:") (forward-line -1))
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+ (forward-line)
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+ ;; For the rest of the code in this file we are based at the
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+ ;; beginning of the first #+R line
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+
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+ ;; FIXME: if point is at the beginning of the #+RR? lines when
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+ ;; this function is called, then tabular output gets inserted,
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+ ;; leaving point up at the top of the tabular output.
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+
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+ (let* ((options (org-R-get-options))
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+ (code (org-R-construct-code options))
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+ (infile (plist-get options :infile))
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+ (ext (if infile (file-name-extension infile)))
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+ csv-file)
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+
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+ (if (string-equal ext "csv")
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+ (setq csv-file infile)
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+ (setq csv-file
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+ (org-R-export-to-csv
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+ (make-temp-file "org-R-tmp" nil ".csv") options)))
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+
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+ (org-R-eval code csv-file options)
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+
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+ (delete-other-windows) ;; FIXME
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+ (if (plist-get options :showcode) (org-R-showcode code)))))
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+
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+(defun org-R-apply-throughout-subtree ()
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+ "Call org-R-apply in every org-R block in current subtree."
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+ ;; This currently relies on re-search-forward leaving point after
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+ ;; the #+RR?: If point were at the beginning of the line, then
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+ ;; tabular input would get inserted leaving point above the #+RR?:,
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+ ;; and this would loop infinitely. Same for org-R-apply-to-buffer.
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+ (interactive)
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+ (save-excursion
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+ (org-back-to-heading)
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+ (while (re-search-forward
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+ "^#\\+RR?:"
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+ (save-excursion (org-end-of-subtree)) t)
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+ (org-R-apply)
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+ (forward-line)
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+ (while (looking-at "#\\+RR?")
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+ (forward-line)))))
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+
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+(defun org-R-apply-throughout-buffer ()
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+ "Call org-R-apply in every org-R block in the buffer."
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+ (interactive)
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+ (save-excursion
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+ (goto-char (point-min))
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+ (while (re-search-forward "^#\\+RR?:" nil t)
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+ (org-R-apply)
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+ (forward-line)
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+ (while (looking-at "#\\+RR?")
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+ (forward-line)))))
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+
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+(defun org-R-construct-code (options)
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+ "Construct the R function that implements the requested
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+behaviour.
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+The body of this function derives from two sources:
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+
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+1. Explicit R code which is read from lines starting with
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+#+RR: by org-R-get-user-code, and
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+
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+2. Off-the-shelf code corresponding to options specified in the
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+#+R: line. This code is constructed by
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+org-R-off-the-shelf-code."
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+ (let ((user-code (org-R-get-user-code))
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+ (action (plist-get options :action)))
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+
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+ (if (or (eq action 'tabulate) (eq action 'transpose))
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+ (setq options (plist-put options :output-to-buffer t)))
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+ (format "function(x){%sx}"
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+ (concat
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+ (when user-code (concat user-code ";"))
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+ (when action (concat (org-R-off-the-shelf-code options) ";"))))))
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+
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+(defun org-R-get-user-code (&optional R)
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+ "Read user-supplied R code from #+RR: lines."
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+ (let ((case-fold-search t))
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+ (save-excursion
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+ (while (looking-at "^#\\+\\(RR?:\\) *\\(.*\\)")
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+ (if (string= "RR:" (match-string 1))
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+ (setq R (concat R (when R ";") (match-string 2))))
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+ (forward-line))))
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+ R)
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+
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+(defun org-R-off-the-shelf-code (options)
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+ "Return R code implementing the actions requested in the
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+#+R: lines."
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+
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+ ;; This is a somewhat long function as it deals with several
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+ ;; different cases, corresponding to all the off-the-shelf actions
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+ ;; that have been implemented.
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+
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+ (let* ((action (plist-get options :action))
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+ (cols (plist-get options :columns))
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+ (ncols (org-R-number-of-columns cols))
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+ (nxcols (nth 0 ncols))
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+ (nycols (nth 1 ncols))
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+ (cols-R (org-R-make-index-vectors cols))
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+ (xcols-R (nth 0 cols-R))
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+ (ycols-R (nth 1 cols-R))
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+ seq args largs extra-code title colour matrix-index)
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+
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+ ;; I want this to affect options outside this function. Will it
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+ ;; necessarily do so? (not if plist-put adds to head of the
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+ ;; plist?)
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+ (setq options (plist-put options :nxcols nxcols))
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+
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+ (cond ((eq action 'points)
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+ (setq action 'plot)
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+ (setq options (plist-put options :lines nil)))
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+ ((eq action 'lines)
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+ (setq action 'plot)
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+ (setq options (plist-put options :lines t))))
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+
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+ (if (and (setq title (plist-get options :title)) (symbolp title))
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+ (setq title symbol-name title))
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+
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+ (setq args (plist-put args :main (concat "\"" title "\"")))
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+
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+ (if (setq colour (or (plist-get options :colour)
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+ (plist-get options :color)
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+ (plist-get options :col)))
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+ (setq args
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+ (plist-put args :col
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+ (concat "\"" (if (symbolp colour) (symbol-name colour) colour) "\""))))
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+
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+ (setq largs
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+ (if (setq legend (plist-get options :legend))
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+ (plist-put largs :x
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+ (concat "\"" (if (symbolp legend) (symbol-name legend) legend) "\""))
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+ (plist-put largs :x "\"topright\"")))
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+
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+ (cond
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+ ((null ycols-R)
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+ ;; single set of columns; implicit x values
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+ (if (null xcols-R)
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+ (setq xcols-R "" matrix-index "")
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+ (setq matrix-index (concat "," xcols-R)))
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+ (cond
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'barplot)
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+ (if (eq nxcols 1)
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+ (progn
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+ (setq args (plist-put args :names.arg "rownames(x)"))
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+ (setq args (org-R-set-user-supplied-args args (plist-get options :args)))
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+ (format org-R-skeleton-funcall-1-arg
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+ "barplot" xcols-R
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+ (concat ", " (org-R-plist-to-R-args args))))
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+
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+ (setq args (plist-put args :names.arg "colnames(x)"))
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+ (setq args (plist-put args :col "seq(nrow(x))"))
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+ (setq args (plist-put args :beside "TRUE"))
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+
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+ (setq largs (plist-put largs :bty "\"n\""))
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+ ;; (setq largs (plist-put largs :lwd 10))
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+ (setq largs (plist-put largs :col "seq(nrow(x))"))
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+ (setq largs (plist-put largs :legend "rownames(x)"))
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+
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+ (setq args (org-R-set-user-supplied-args args (plist-get options :args)))
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+
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+ (concat (format org-R-skeleton-funcall-1-arg
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+ "barplot(as.matrix" matrix-index
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+ (concat "), " (org-R-plist-to-R-args args)))
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+ "; legend(" (org-R-plist-to-R-args largs) ")")))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'density)
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+ (if (and nxcols (> nxcols 1))
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+ (error "Multiple columns not implemented for action:%s" action))
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+
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+ (setq args (plist-put args :xlab (concat "colnames(x)["xcols-R"]")))
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+ (setq args (org-R-set-user-supplied-args args (plist-get options :args)))
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+
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+ (format org-R-skeleton-funcall-1-arg
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+ "plot(density" matrix-index
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+ (concat "), " (org-R-plist-to-R-args args))))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'hist)
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+ (if (and nxcols (> nxcols 1))
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+ (error "Multiple columns not implemented for action:%s" action))
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+ (setq args (plist-put args :xlab (concat "colnames(x)["xcols-R"]")))
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+ (setq args (org-R-set-user-supplied-args args (plist-get options :args)))
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+ (setq args (concat ", " (org-R-plist-to-R-args args)))
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+ (format org-R-skeleton-funcall-1-arg "hist" matrix-index args))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'image)
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+ (format org-R-skeleton-funcall-1-arg "image(as.matrix" matrix-index ")"))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'plot)
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+ (setq seq (concat "seq_along("xcols-R")"))
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+
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+ (setq args (plist-put args :type (if (plist-get options :lines) "\"l\"" "\"p\"")))
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+ (setq args (plist-put args :ylab (concat "colnames(x)["xcols-R"]")))
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+ (setq args (concat ", " (org-R-plist-to-R-args args)))
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+
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+ (concat (format org-R-skeleton-funcall-1-arg
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+ (if (eq nxcols 1) "plot" "matplot") matrix-index args)
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+ extra-code))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'tabulate)
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+ (concat
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+ (if (plist-get options :sort)
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+ (format org-R-skeleton-funcall-1-arg
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+ "x <- sort(table" xcols-R "), decreasing=TRUE")
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+ (format org-R-skeleton-funcall-1-arg "x <- table" matrix-index ""))
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+ (if (eq nxcols 1) "; x <- data.frame(value=names(x), count=x[])")))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'transpose)
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+ (format org-R-skeleton-funcall-1-arg "x <- t" matrix-index ""))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ;; Don't recognise action: option, try applying it as the name of an R function.
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+
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+ (t (format org-R-skeleton-funcall-1-arg
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+ (concat "x <- " (symbol-name action)) matrix-index ""))))
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+
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+ ;;----------------------------------------------------------------------
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+
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+ (ycols-R
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+ ;; x and y columns specified
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+ (cond
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+
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+ ;;----------------------------------------------------------------------
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+
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+ ((eq action 'plot)
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+ (unless (eq nxcols 1) (error "Multiple x-columns not implemented for action:plot"))
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+
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+ (setq args
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+ (plist-put
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+ args :ylab
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+ (concat "if(length("ycols-R") == 1) colnames(x)["ycols-R"] else ''")))
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+ (setq args (plist-put args :xlab (concat "colnames(x)["xcols-R"]")))
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+
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+ (setq args (plist-put args :type (if (plist-get options :lines) "\"l\"" "\"p\"")))
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+
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+ (setq args (concat ", " (org-R-plist-to-R-args args)))
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+ (setq seq (concat "seq_along("ycols-R")"))
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+
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+ (setq largs (plist-put largs :col seq))
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+ (setq largs (plist-put largs :lty seq))
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+ (setq largs (plist-put largs :bty "\"n\""))
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+ (setq largs (plist-put largs :legend (concat "colnames(x)["ycols-R"]")))
|
|
|
+
|
|
|
+ (setq extra-code
|
|
|
+ (concat "; "
|
|
|
+ "if(length("ycols-R") > 1) "
|
|
|
+ "legend(" (org-R-plist-to-R-args largs) ")"))
|
|
|
+
|
|
|
+ (concat (format org-R-skeleton-funcall-2-args
|
|
|
+ (if (and (eq nxcols 1) (eq nycols 1)) "plot" "matplot")
|
|
|
+ xcols-R ycols-R args)
|
|
|
+ extra-code))
|
|
|
+
|
|
|
+ ;;----------------------------------------------------------------------
|
|
|
+
|
|
|
+ (t (error "action:%s requires a single set of columns" (symbol-name action))))))))
|
|
|
+
|
|
|
+(defun org-R-set-user-supplied-args (args user-args)
|
|
|
+ "Set user-supplied values in arguments plist."
|
|
|
+ (while (setq prop (pop user-args))
|
|
|
+ (setq args (plist-put args prop (pop user-args))))
|
|
|
+ args)
|
|
|
+
|
|
|
+(defun org-R-plist-to-R-args (plist)
|
|
|
+ "Convert a plist into a string of R arguments."
|
|
|
+ (let (arg-string arg)
|
|
|
+ (while (setq arg (pop plist))
|
|
|
+ (string-match ":\\(\.*\\)" (symbol-name arg))
|
|
|
+ (setq arg (match-string 1 (symbol-name arg)))
|
|
|
+ (setq arg-string
|
|
|
+ (concat
|
|
|
+ (if arg-string (concat arg-string ", "))
|
|
|
+ (format "%s=%s" arg (pop plist)))))
|
|
|
+ arg-string))
|
|
|
+
|
|
|
+(defun org-R-alist-to-R-args (alist)
|
|
|
+ "Convert an alist of (argument . val) pairs into a string of R arguments.
|
|
|
+The alist is something like
|
|
|
+ '((arg1 . 1)
|
|
|
+ (arg2 . a))
|
|
|
+This isn't used, but it seems much nicer than
|
|
|
+my plist equivalent. Is there a better way to write the plist
|
|
|
+version?
|
|
|
+"
|
|
|
+ (mapconcat
|
|
|
+ 'identity
|
|
|
+ (mapcar (lambda(pair) (format "%s = %s" (car pair) (cdr pair))) alist)
|
|
|
+ ", "))
|
|
|
+
|
|
|
+(defun org-R-make-index-vectors (cols)
|
|
|
+ "Construct R indexing vectors as strings from lisp form.
|
|
|
+
|
|
|
+COLS is the lisp form given by the `columns:' option. It may
|
|
|
+take the following forms:
|
|
|
+
|
|
|
+1. integer atom - the number of the column
|
|
|
+2. symbol/string atom - the name of the column
|
|
|
+3. list of length 1 - same as 1 or 2 above
|
|
|
+4. list of length > 1 - specification of multiple columns as 1 or 2 above, unless it is
|
|
|
+5. list of 2 lists - each list specifies (possibly multiple) columns
|
|
|
+
|
|
|
+In cases 1-4 this function returns a list of length 1, containing
|
|
|
+the R index vector as a string. In case 5 this function returns a
|
|
|
+list of two such index vectors.
|
|
|
+
|
|
|
+In cases 1 - 4, when a bivariate plot is requested such as by
|
|
|
+`action:lines', the x values are implicit, i.e
|
|
|
+1,2,...,number-of-rows.
|
|
|
+
|
|
|
+In case 4, an attempt is made to do something sensible with the
|
|
|
+multiple columns, e.g. for `action:lines' they will be plotted
|
|
|
+together on the same graph against the implicit x values, and for
|
|
|
+`action:barplot' the bars corresponding to a single row will be
|
|
|
+stacked on top of each other, or placed side by side, depending
|
|
|
+on the value of the `beside' option.
|
|
|
+
|
|
|
+For `action:tabulate', if 2 columns are selected, a
|
|
|
+two-dimensional table is created. If more than 2, then the
|
|
|
+appropriately dimensioned table is computed and inserted using
|
|
|
+the standard text representation of multi-dimensional arrays used
|
|
|
+by R (as org does not currently have tables of dimension > 2).
|
|
|
+
|
|
|
+The straightforward case of case 5 is that both lists are of
|
|
|
+length 1. For `action:plot' and `action:lines' these specify the
|
|
|
+y and x coordinates of the points to be plotted or joined by
|
|
|
+lines.
|
|
|
+
|
|
|
+The intention is that `org-R-apply' does something
|
|
|
+corresponding to what would happen if you did the following in R:
|
|
|
+
|
|
|
+fun(x=tab[,xcols], y=tab[,ycols])
|
|
|
+
|
|
|
+where fun is the R function implementing the desired
|
|
|
+action (plotting/computation), tab is the org table, xcols are
|
|
|
+the columns specified in cases 1-4 above, and ycols are the
|
|
|
+second set of columns which might have been specified under case
|
|
|
+5 above. For relevant R documentation see the help page
|
|
|
+associated with the function xy.coords, e.g. by typing ?xy.coords
|
|
|
+at the R prompt.
|
|
|
+
|
|
|
+The following won't work with case 5: `tabulate'
|
|
|
+"
|
|
|
+ (defun org-R-make-index-vector (cols)
|
|
|
+ "Return the R indexing vector (as a string) corresponding to
|
|
|
+the lisp form COLS. In this function, COLS is a either a list of
|
|
|
+atoms, or an atom, i.e. in the form of cases 1-4"
|
|
|
+ (when cols
|
|
|
+ (let (to-stringf)
|
|
|
+ (unless (listp cols) (setq cols (list cols)))
|
|
|
+ (setq to-stringf
|
|
|
+ (cond ((car (mapcar 'symbolp cols))
|
|
|
+ (lambda (symbol) (concat "\"" (symbol-name symbol) "\"")))
|
|
|
+ ((car (mapcar 'integerp cols))
|
|
|
+ 'int-to-string)
|
|
|
+ ((car (mapcar 'stringp cols))
|
|
|
+ (lambda (string) (concat "\"" string "\"")))
|
|
|
+ (t (error "Column selection should be symbol, integer or string: %S" cols))))
|
|
|
+ (concat (when (> (length cols) 1) "c(")
|
|
|
+ (mapconcat to-stringf cols ",")
|
|
|
+ (when (> (length cols) 1) ")")))))
|
|
|
+
|
|
|
+ (if (and (listp cols) (listp (car cols)))
|
|
|
+ (mapcar 'org-R-make-index-vector cols) ;; case 5
|
|
|
+ (list (org-R-make-index-vector cols)))) ;; other cases
|
|
|
+
|
|
|
+(defun org-R-number-of-columns (cols)
|
|
|
+ (defun f (c) (if (listp c) (length c) 1))
|
|
|
+ (if (and (listp cols) (listp (car cols)))
|
|
|
+ (mapcar 'f cols)
|
|
|
+ (list (f cols))))
|
|
|
+
|
|
|
+(defun org-R-eval (R-function csv-file options)
|
|
|
+ "Apply an R function to tabular data and receive output as an org table.
|
|
|
+
|
|
|
+R-FUNCTION is a string; it may be simply the name of an
|
|
|
+appropriate R function (e.g. \"summary\", \"plot\"), or a
|
|
|
+user-defined anonymous function of the form
|
|
|
+\"(function(data.frame) {...})\". It will receive as its first
|
|
|
+argument the org table as an R 'data frame' -- a table-like
|
|
|
+structure which can have columns containing different types of
|
|
|
+data -- numeric, character etc.
|
|
|
+
|
|
|
+The R function may produce graphical and/or text output. If it
|
|
|
+produces text output, and the replace:t is specified, and if
|
|
|
+there is a table immediately above the #+R lines, then it is
|
|
|
+replaced by the text output. Otherwise the text output is
|
|
|
+inserted above the #+R lines.
|
|
|
+"
|
|
|
+ (let ((transit-buffer "org-R-transit")
|
|
|
+ (infile (plist-get options :infile))
|
|
|
+ (output-file (plist-get options :outfile))
|
|
|
+ (title (plist-get options :title))
|
|
|
+ output-format graphics-output-file width height)
|
|
|
+
|
|
|
+ (unless (not output-file)
|
|
|
+ ;; We are writing output to file. Determine file format and
|
|
|
+ ;; location, and open graphics device if necessary.
|
|
|
+ (if (string-match
|
|
|
+ "\\(.*\.\\)?\\(org\\|png\\|jpg\\|jpeg\\|pdf\\|ps\\|bmp\\|tiff\\)$"
|
|
|
+ output-file)
|
|
|
+ (setq output-format (match-string 2 output-file))
|
|
|
+ (error "Did not recognise file name suffix %s as available output format"
|
|
|
+ (match-string 2 output-file)))
|
|
|
+ (unless (match-string 1 output-file)
|
|
|
+ ;; only suffix provided: store in org-attach dir
|
|
|
+ (require 'org-attach)
|
|
|
+ (let ((temporary-file-directory (org-attach-dir t)))
|
|
|
+ (setq output-file
|
|
|
+ (make-temp-file
|
|
|
+ "org-R-output-" nil (concat "." output-format)))))
|
|
|
+ (if (eq output-format "jpg") (setq output-format "jpeg"))
|
|
|
+ (setq graphics-output-file (not (string-equal output-format "org")))
|
|
|
+ (if graphics-output-file ;; open the graphics device
|
|
|
+ (ess-execute
|
|
|
+ (concat output-format "(file=\"" output-file "\""
|
|
|
+ (if (setq width (plist-get options :width))
|
|
|
+ (format ", width=%d" width))
|
|
|
+ (if (setq height (plist-get options :height))
|
|
|
+ (format ", height=%d" height)) ")"))))
|
|
|
+
|
|
|
+ ;; Apply R code to table (which is now stored as a csv file)
|
|
|
+ ;; does it matter whether this uses ess-command or ess-execute?
|
|
|
+
|
|
|
+ ;; First evaluate function definition for R -> org table conversion
|
|
|
+ (ess-execute (replace-regexp-in-string "\n" " " org-R-write-org-table-def)
|
|
|
+ nil transit-buffer)
|
|
|
+
|
|
|
+ ;; FIXME: why not eval the function def together with the function call
|
|
|
+ ;; as in the commented out line below (it didn't work for some reason)
|
|
|
+ (ess-execute
|
|
|
+ (concat
|
|
|
+ ;; (replace-regexp-in-string "\n" " " org-R-write-org-table-def) ";"
|
|
|
+ (org-R-make-expr R-function csv-file options)) nil transit-buffer)
|
|
|
+
|
|
|
+ (save-excursion
|
|
|
+ (set-buffer (concat "*" transit-buffer "*"))
|
|
|
+ (unless (or (looking-at "$")
|
|
|
+ (string-equal (buffer-substring-no-properties 1 2) "|"))
|
|
|
+ (error "Error in R evaluation:\n%s" (buffer-string))))
|
|
|
+
|
|
|
+
|
|
|
+ (if csv-file
|
|
|
+ (unless (and infile
|
|
|
+ (string-equal (file-name-extension infile) "csv"))
|
|
|
+ (delete-file csv-file)))
|
|
|
+
|
|
|
+ (if graphics-output-file (ess-execute "dev.off()")) ;; Close graphics device
|
|
|
+
|
|
|
+ (unless (or graphics-output-file
|
|
|
+ (not (plist-get options :output-to-buffer)))
|
|
|
+ ;; Send tabular output to a org buffer as new org
|
|
|
+ ;; table. Recall that we are currently at the beginning of the
|
|
|
+ ;; first #+R line
|
|
|
+ (if (and output-file graphics-output-file)
|
|
|
+ (error "output-to-buffer and graphics-output-file both t"))
|
|
|
+
|
|
|
+ (save-excursion
|
|
|
+ (if output-file
|
|
|
+ (progn (set-buffer (find-file-noselect output-file))
|
|
|
+ (delete-region (point-min) (point-max)))
|
|
|
+ (if (plist-get options :replace)
|
|
|
+ (progn ;; kill a table iff in one or one ends on the previous line
|
|
|
+ (delete-region (org-table-begin) (org-table-end))
|
|
|
+ (save-excursion
|
|
|
+ (forward-line -1)
|
|
|
+ (if (looking-at "#\\+TBLNAME")
|
|
|
+ (delete-region (point) (1+ (point-at-eol))))))))
|
|
|
+ (if title (insert "#+TBLNAME:" title "\n"))
|
|
|
+ (insert-buffer-substring (concat "*" transit-buffer "*"))
|
|
|
+ (org-table-align)
|
|
|
+ (if output-file (save-buffer))))
|
|
|
+
|
|
|
+ ;; We might be linking to graphical output, or to org output in
|
|
|
+ ;; another file. Either way, point is still at the beginning of
|
|
|
+ ;; the first #+R line.
|
|
|
+ (unless (not output-file)
|
|
|
+ (save-excursion
|
|
|
+ (forward-line -1)
|
|
|
+ (if (looking-at "\\[\\[file:")
|
|
|
+ (delete-region (point) (1+ (point-at-eol)))))
|
|
|
+ (insert (org-make-link-string
|
|
|
+ (concat "file:" output-file)
|
|
|
+ (unless (plist-get options :inline)
|
|
|
+ (or title (concat output-format " output")))) "\n"))
|
|
|
+
|
|
|
+ (kill-buffer (concat "*" transit-buffer "*"))))
|
|
|
+
|
|
|
+
|
|
|
+(defun org-R-export-to-csv (csv-file options)
|
|
|
+ "Find and export org table to csv.
|
|
|
+
|
|
|
+If the intable: option has not been supplied, then the table must
|
|
|
+end on the line immediately above the #+R lines. Otherwise,
|
|
|
+the remote table referenced by the intable: option is found using
|
|
|
+org-R-find-table. If options:infile has been set then this is the
|
|
|
+org file containing the table. See the docstring of
|
|
|
+org-R-find-table for details."
|
|
|
+ (let ((tbl-name-or-id (plist-get options :intable))
|
|
|
+ (org-file (plist-get options :infile)) tbl-marker)
|
|
|
+
|
|
|
+ (if (and org-file
|
|
|
+ (not (string-equal (file-name-extension org-file) "org")))
|
|
|
+ (error "File %s extension is not .csv so should be .org"))
|
|
|
+
|
|
|
+ (save-excursion
|
|
|
+ (if tbl-name-or-id
|
|
|
+ ;; a remote table has been specified -- move into it
|
|
|
+ (progn
|
|
|
+ (if org-file (set-buffer (find-file-noselect org-file)))
|
|
|
+ (setq tbl-marker (org-R-find-table tbl-name-or-id 'marker))
|
|
|
+ (set-buffer (marker-buffer tbl-marker))
|
|
|
+ (goto-char (marker-position tbl-marker)))
|
|
|
+ (forward-line -1)) ;; move into table above
|
|
|
+ (if (looking-at "[ \t]*|")
|
|
|
+ (progn (org-table-export csv-file "orgtbl-to-csv") csv-file)
|
|
|
+ nil))))
|
|
|
+
|
|
|
+(defun org-R-find-table (name-or-id &optional markerp)
|
|
|
+ "Return location of a table.
|
|
|
+
|
|
|
+NAME-OR-ID may be the name of a
|
|
|
+table in the current file as set by a \"#+TBLNAME:\" directive.
|
|
|
+The first table following this line will then be used.
|
|
|
+Alternatively, it may be an ID referring to any entry, perhaps in
|
|
|
+a different file. In this case, the first table in that entry
|
|
|
+will be referenced. The location is returned as a marker pointing
|
|
|
+to the beginning of the first line of the table.
|
|
|
+
|
|
|
+This is taken from the first part of org-table-get-remote-range
|
|
|
+in org-table.el.
|
|
|
+"
|
|
|
+ (cond
|
|
|
+ ((symbolp name-or-id) (setq name-or-id (symbol-name name-or-id)))
|
|
|
+ ((numberp name-or-id) (setq name-or-id (number-to-string name-or-id))))
|
|
|
+ (save-match-data
|
|
|
+ (let ((id-loc nil) (case-fold-search t) buffer loc)
|
|
|
+ (save-excursion
|
|
|
+ (save-restriction
|
|
|
+ (widen)
|
|
|
+ (save-excursion
|
|
|
+ (goto-char (point-min))
|
|
|
+ (if (re-search-forward
|
|
|
+ (concat "^#\\+TBLNAME:[ \t]*" (regexp-quote name-or-id) "[ \t]*$")
|
|
|
+ nil t)
|
|
|
+ ;; OK, we've found a matching table name in this buffer.
|
|
|
+ (setq buffer (current-buffer) loc (match-beginning 0))
|
|
|
+ ;; It's not a table name in this buffer. It must be an entry id.
|
|
|
+ ;; obtain a marker pointing to it.
|
|
|
+ (setq id-loc (org-id-find name-or-id 'marker)
|
|
|
+ buffer (marker-buffer id-loc)
|
|
|
+ loc (marker-position id-loc))
|
|
|
+ (move-marker id-loc nil))) ;; disable the marker
|
|
|
+ ;; (switch-to-buffer buffer)
|
|
|
+ (set-buffer buffer)
|
|
|
+ ;; OK, so now we're in the right buffer, and loc is either
|
|
|
+ ;; the beginning of the #+TBLNAME line, or the location of the entry
|
|
|
+ ;; either way we need to search forward to get to the beginning of the table
|
|
|
+ (save-excursion
|
|
|
+ (save-restriction
|
|
|
+ (widen)
|
|
|
+ (goto-char loc)
|
|
|
+ (forward-char 1)
|
|
|
+ ;; The following regexp search finds the beginning of
|
|
|
+ ;; the next table in this entry. If it gets to the next
|
|
|
+ ;; entry before the next table, then it signals failure.
|
|
|
+ (unless (and (re-search-forward "^\\(\\*+ \\)\\|[ \t]*|" nil t)
|
|
|
+ (not (match-beginning 1)))
|
|
|
+ (error "Cannot find a table at NAME or ID %s" name-or-id))
|
|
|
+ (if markerp
|
|
|
+ (move-marker (make-marker) (point-at-bol) (current-buffer))
|
|
|
+ (error "Option to return cons cell not implemented.
|
|
|
+ It should return (file-name . position) to be
|
|
|
+ consistent with functions in org-id.el")))))))))
|
|
|
+
|
|
|
+(defun org-R-make-expr (R-function csv-file options)
|
|
|
+ "Construct R code to read data, analyse it and write output."
|
|
|
+
|
|
|
+ (let ((rownames (plist-get options :rownames))
|
|
|
+ (colnames (plist-get options :colnames))
|
|
|
+ (action (plist-get options :action))
|
|
|
+ (replace (plist-get options :replace)))
|
|
|
+
|
|
|
+ (if (and csv-file (symbolp csv-file))
|
|
|
+ (setq csv-file (symbol-name csv-file)))
|
|
|
+
|
|
|
+ (format "write.org.table((%s)(%s), write.rownames=%s)"
|
|
|
+ R-function
|
|
|
+ (if csv-file
|
|
|
+ (format
|
|
|
+ "read.csv(\"%s\", header=%s, row.names=%s)"
|
|
|
+ csv-file
|
|
|
+
|
|
|
+ ;; Do we treat first row as colnames? Yes by default
|
|
|
+ ;; FIXME: should really check for hline
|
|
|
+ (if colnames "TRUE" "FALSE")
|
|
|
+
|
|
|
+ ;; Do we use a column as rownames? Not unless rownames: is specified
|
|
|
+ (if rownames "1" "NULL"))
|
|
|
+ "NULL")
|
|
|
+
|
|
|
+ ;; Do we write rownames into org table?
|
|
|
+ (cond ((eq action 'tabulate)
|
|
|
+ (if (eq (plist-get options :nxcols) 1) "FALSE" "TRUE"))
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+ ((eq action 'transpose) (if colnames "TRUE" "FALSE"))
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+ (rownames "TRUE")
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+ (t "TRUE")))))
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+
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+(defun org-R-get-options ()
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|
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+ "Parse the #+R: lines and return the options and values as a p-list."
|
|
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+ (let ((opts '(
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+ (:infile . "infile")
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+ (:intable . "intable")
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+ (:rownames . "rownames")
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+ (:colnames . "colnames")
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+ (:columns . "columns")
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+
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+ (:action . "action")
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+ (:args . "args")
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+
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+ (:outfile . "outfile")
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+ (:replace . "replace")
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+ (:title . "title")
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+ (:legend . "legend")
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+ (:colour . "colour")
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+ (:color . "color")
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+ (:col . "col")
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+ (:height . "height")
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+ (:width . "width")
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+ (:lines . "lines")
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+ (:sort . "sort")
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|
+ (:inline . "inline")
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+
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+ (:output-to-buffer . "output-to-buffer")
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+
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+ (:showcode . "showcode")))
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|
|
+ (regexp ":\\(\"[^\"]*\"\\|(([^)]*) *([^)]*))\\|([^)]*)\\|[^ \t\n\r;,.]*\\)")
|
|
|
+ (case-fold-search t) p)
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|
|
+
|
|
|
+ ;; FIXME: set default options properly
|
|
|
+ (setq p (plist-put p :output-to-buffer t)) ;; FIXME: hack: null options plist is bad news
|
|
|
+ (setq p (plist-put p :replace t))
|
|
|
+ (setq p (plist-put p :rownames nil))
|
|
|
+ (setq p (plist-put p :colnames t))
|
|
|
+ (setq p (plist-put p :inline nil))
|
|
|
+
|
|
|
+ (save-excursion
|
|
|
+ (while (looking-at "^#\\+\\(RR?:+\\) *\\(.*\\)")
|
|
|
+ (if (string= "R:" (match-string 1))
|
|
|
+ (setq p (org-R-add-options-to-plist p (match-string 2) opts regexp)))
|
|
|
+ (forward-line)))
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|
|
+ p))
|
|
|
+
|
|
|
+(defun org-R-add-options-to-plist (p opt-string op regexp)
|
|
|
+ "Parse a #+R: line and set values in the property list p.
|
|
|
+This function is adapted from similar functions in org-exp.el
|
|
|
+and org-plot.el. It might be a good idea to have a single
|
|
|
+function serving these three files' needs."
|
|
|
+ ;; Adapted from org-exp.el and org-plot.el
|
|
|
+ (let (o)
|
|
|
+ (when opt-string
|
|
|
+ (while (setq o (pop op))
|
|
|
+ (if (string-match
|
|
|
+ (concat (regexp-quote (cdr o)) regexp)
|
|
|
+ opt-string)
|
|
|
+ (setq p (plist-put p (car o)
|
|
|
+ (car (read-from-string
|
|
|
+ (match-string 1 opt-string)))))))))
|
|
|
+ p)
|
|
|
+
|
|
|
+
|
|
|
+(defun org-R-sanitise-options (options)
|
|
|
+ (error "not used yet")
|
|
|
+ (let (should-be-strings '(title legend colour color col csv)))
|
|
|
+ )
|
|
|
+(defun org-R-showcode (R)
|
|
|
+ "Display R function constructed by org-R in a new R-mode
|
|
|
+buffer."
|
|
|
+ (split-window-vertically)
|
|
|
+ (switch-to-buffer "*org-table.R*")
|
|
|
+ (kill-region (point-min) (point-max))
|
|
|
+ (R-mode)
|
|
|
+ (insert (replace-regexp-in-string
|
|
|
+ ";" "\n" (replace-regexp-in-string "\\([{}]\\)" "\n\\1\n" R)))
|
|
|
+ ;; (mark-whole-buffer)
|
|
|
+ ;; (indent-region)
|
|
|
+ ;; why doesn't that do what I hoped?
|
|
|
+ )
|
|
|
+
|
|
|
+(defun org-R-get-remote-range (name-or-id form)
|
|
|
+ "Get a field value or a list of values in a range from table at ID.
|
|
|
+
|
|
|
+This is a refactoring of Carsten's original version. I have
|
|
|
+extracted the first bit of his function and named it
|
|
|
+org-R-find-table (which would presumably be called something like
|
|
|
+org-table-find-table or org-id-find-table if this were accepted).
|
|
|
+
|
|
|
+---
|
|
|
+
|
|
|
+Get a field value or a list of values in a range from table at ID.
|
|
|
+
|
|
|
+NAME-OR-ID may be the name of a table in the current file as set by
|
|
|
+a \"#+TBLNAME:\" directive. The first table following this line
|
|
|
+will then be used. Alternatively, it may be an ID referring to
|
|
|
+any entry, possibly in a different file. In this case, the first table
|
|
|
+in that entry will be referenced.
|
|
|
+FORM is a field or range descriptor like \"@2$3\" or or \"B3\" or
|
|
|
+\"@I$2..@II$2\". All the references must be absolute, not relative.
|
|
|
+
|
|
|
+The return value is either a single string for a single field, or a
|
|
|
+list of the fields in the rectangle."
|
|
|
+
|
|
|
+ (let ((tbl-marker (org-R-find-table name-or-id 'marker))
|
|
|
+ org-table-column-names org-table-column-name-regexp
|
|
|
+ org-table-local-parameters org-table-named-field-locations
|
|
|
+ org-table-current-line-types org-table-current-begin-line
|
|
|
+ org-table-current-begin-pos org-table-dlines
|
|
|
+ org-table-hlines org-table-last-alignment
|
|
|
+ org-table-last-column-widths org-table-last-alignment
|
|
|
+ org-table-last-column-widths tbeg)
|
|
|
+
|
|
|
+ (save-excursion
|
|
|
+ (set-buffer (marker-buffer tbl-marker))
|
|
|
+ (goto-char (marker-position tbl-marker))
|
|
|
+ (org-table-get-specials)
|
|
|
+ (setq form (org-table-formula-substitute-names form))
|
|
|
+ (if (and (string-match org-table-range-regexp form)
|
|
|
+ (> (length (match-string 0 form)) 1))
|
|
|
+ (save-match-data
|
|
|
+ (org-table-get-range (match-string 0 form) (point) 1))
|
|
|
+ form))))
|
|
|
+
|
|
|
+(provide 'org-R)
|
Carsten Dominik