Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]

[Eric Schulte <schulte.eric@gmail.com>]

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Hi Feiming,

The "width" and "height" header arguments are passed to R to affect the
size of the generated file e.g.,

  png(filename="a1.png",width=500,height=500)

however they do not affect the generated latex code.  Luckily Org-mode
does support passing information like image width to latex figures.  See
my attached version of your test file which uses #+ATTR_LaTeX lines to
specify the width during LaTeX export.

Best -- Eric


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#+TITLE:test
#+BABEL: :session *R* :results output graphics :exports both 

#+source: plot1
#+begin_src R :file a1.png :width 500 :height 500
  a <- b <- 1:10
  plot(a, b)
#+end_src

#+ATTR_LaTeX: width=500px
#+results: plot1
[[file:a1.png]]

#+source: plot2
#+begin_src R :file a2.png :width 1000 :height 1000
  plot(a, b)
#+end_src

#+ATTR_LaTeX: width=100px
#+results: plot2
[[file:a2.png]]

#+source: plot3
#+begin_src R :file a3.pdf :width 5 :height 5
  a <- b <- 1:10
  plot(a, b)
#+end_src

#+ATTR_LaTeX: width=5px
#+results: plot3
[[file:a3.pdf]]

#+source: plot4
#+begin_src R :file a4.pdf :width 10 :height 10
  plot(a, b)
#+end_src

#+ATTR_LaTeX: width=10
#+results: plot4
[[file:a4.pdf]]

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Feiming Chen <feimingchen@yahoo.com> writes:

> Hi, I like org-mode and org-babel mode very much, but recently I am  having problems outputting R graphics to LaTeX report with
> Org-Babel mode.  Attached is my test file, where I am generating 4
> simple plots of different sizes and format (.png or .pdf).  The HTML
> export is satisfactory, however, the LaTeX export (C-c C-e l) presents two problems: 
>
>     1.  All 4 plots have the same size (10em) which is different from the
>     header specification and is too small.
>
> \includegraphics[width=10em]{a1.png} ...
> \includegraphics[width=10em]{a2.png} ...
> \includegraphics[width=10em]{a3.pdf} ...
> \includegraphics[width=10em]{a4.pdf} ...
>
>     2. While exporting to PDF file, the R code is mysteriously lost in
>     the R execution for the PDF output of the plots and the compilation failed correspondingly: 
>
>> pdf(file="a3.pdf",width=5,height=5)
>> 
>> dev.off()
>> pdf(file="a4.pdf",width=10,height=10)
>>
>> dev.off()
>
>
> Hopefully you can replicate my errors and help me on this.  Thanks a
> lot!
>
> Best regards, 
> Feiming Chen
>
> ____________________________________________________________
>
>
> Emacs  : GNU Emacs 23.2.1 (i386-redhat-linux-gnu, GTK+ Version 2.21.4)
>  of 2010-07-08 on x86-05.phx2.fedoraproject.org
> Package: Org-mode version 7.5
>
> current state:
> ==============
> (setq
>  org-file-apps '((auto-mode . emacs) ("\\.mm\\'" . default)
>          ("\\.x?html?\\'" . "firefox %s") ("\\.pdf\\'" . "evince %s"))
>  org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
>  org-hide-block-startup t
>  org-speed-command-hook '(org-speed-command-default-hook
>               org-babel-speed-command-hook)
>  org-src-fontify-natively t
>  org-babel-load-languages '((emacs-lisp . t) (R . t))
>  org-metaup-hook '(org-babel-load-in-session-maybe)
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
>  org-export-latex-format-toc-function 'org-export-latex-format-toc-default
>  org-tab-first-hook '(org-hide-block-toggle-maybe
>               org-src-native-tab-command-maybe
>               org-babel-hide-result-toggle-maybe)
>  outline-regexp "\\*+ "
>  org-src-mode-hook '(org-src-babel-configure-edit-buffer
>              org-src-mode-configure-edit-buffer)
>  org-confirm-shell-link-function 'yes-or-no-p
>  org-reveal-start-hook '(org-decrypt-entry)
>  org-export-first-hook '(org-beamer-initialize-open-trackers)
>  org-format-latex-header
> "\\documentclass{article}\n\\usepackage[usenames]{color}\n\\usepackage{amsmath}\n\\usepackage[mathscr]{eucal}\n%
> Feiming's Customization
> BEGIN\n\\usepackage[colorlinks=true]{hyperref}\n\\input{/home/chen/lib/math.tex}\n%
> Feiming's Customization END\n\\pagestyle{empty}             % do not
> remove\n[PACKAGES]\n[DEFAULT-PACKAGES]\n% The settings below are
> copied from
> fullpage.sty\n\\setlength{\\textwidth}{\\paperwidth}\n\\addtolength{\\textwidth}{-3cm}\n\\setlength{\\oddsidemargin}{1.5cm}\n\\addtolength{\\oddsidemargin}{-2.54cm}\n\\setlength{\\evensidemargin}{\\oddsidemargin}\n\\setlength{\\textheight}{\\paperheight}\n\\addtolength{\\textheight}{-\\headheight}\n\\addtolength{\\textheight}{-\\headsep}\n\\addtolength{\\textheight}{-\\footskip}\n\\addtolength{\\textheight}{-3cm}\n\\setlength{\\topmargin}{1.5cm}\n\\addtolength{\\topmargin}{-2.54cm}"
>  org-startup-indented t
>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>  org-babel-pre-tangle-hook '(save-buffer)
>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
>           org-cycle-show-empty-lines
>           org-optimize-window-after-visibility-change)
>  org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
>  org-use-speed-commands t
>  org-mode-hook '(turn-on-org-cdlatex
>          (lambda nil
>           (setq org-mouse-context-menu-function
>            (quote org-mouse-context-menu))
>           (when (memq (quote context-menu) org-mouse-features)
>            (org-defkey org-mouse-map [mouse-3] nil)
>            (org-defkey org-mode-map [mouse-3]
>             (quote org-mouse-show-context-menu))
>            )
>           (org-defkey org-mode-map [down-mouse-1]
>            (quote org-mouse-down-mouse))
>           (when (memq (quote context-menu) org-mouse-features)
>            (org-defkey org-mouse-map [C-drag-mouse-1]
>             (quote org-mouse-move-tree))
>            (org-defkey org-mouse-map [C-down-mouse-1]
>             (quote org-mouse-move-tree-start))
>            )
>           (when (memq (quote yank-link) org-mouse-features)
>            (org-defkey org-mode-map [S-mouse-2]
>             (quote org-mouse-yank-link))
>            (org-defkey org-mode-map [drag-mouse-3]
>             (quote org-mouse-yank-link))
>            )
>           (when (memq (quote move-tree) org-mouse-features)
>            (org-defkey org-mouse-map [drag-mouse-3]
>             (quote org-mouse-move-tree))
>            (org-defkey org-mouse-map [down-mouse-3]
>             (quote org-mouse-move-tree-start))
>            )
>           (when (memq (quote activate-stars) org-mouse-features)
>            (font-lock-add-keywords nil
>             (\`
>              (((\, outline-regexp) 0
>                (\`
>             (face org-link mouse-face highlight keymap
>              (\, org-mouse-map))
>             )
>                (quote prepend))
>               )
>              )
>             t)
>            )
>           (when (memq (quote activate-bullets) org-mouse-features)
>            (font-lock-add-keywords nil
>             (\`
>              (("^[    ]*\\([-+*]\\|[0-9]+[.)]\\) +"
>                (1
>             (\`
>              (face org-link keymap (\, org-mouse-map) mouse-face
>               highlight)
>              )
>             (quote prepend))
>                )
>               )
>              )
>             t)
>            )
>           (when (memq (quote activate-checkboxes) org-mouse-features)
>            (font-lock-add-keywords nil
>             (\`
>              (("^[    ]*\\([-+*]\\|[0-9]+[.)]\\) +\\(\\[[ X]\\]\\)"
>                (2
>             (\`
>              (face bold keymap (\, org-mouse-map) mouse-face
>               highlight)
>              )
>             t)
>                )
>               )
>              )
>             t)
>            )
>           (defadvice org-open-at-point
>            (around org-mouse-open-at-point activate)
>            (let ((context (org-context)))
>             (cond ((assq :headline-stars context) (org-cycle))
>              ((assq :checkbox context) (org-toggle-checkbox))
>              ((assq :item-bullet context)
>               (let ((org-cycle-include-plain-lists t)) (org-cycle)))
>              (t ad-do-it))
>             )
>            )
>           )
>          #[nil "\300\301\302\303\304$\207"
>            [org-add-hook change-major-mode-hook org-show-block-all append
>             local]
>            5]
>          #[nil "\300\301\302\303\304$\207"
>            [org-add-hook change-major-mode-hook org-babel-show-result-all
>             append local]
>            5]
>          org-babel-result-hide-spec org-babel-hide-all-hashes)
>  org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-agenda-mode-hook '((lambda nil
>              (setq org-mouse-context-menu-function
>               (quote org-mouse-agenda-context-menu))
>              (org-defkey org-agenda-mode-map [mouse-3]
>               (quote org-mouse-show-context-menu))
>              (org-defkey org-agenda-mode-map [down-mouse-3]
>               (quote org-mouse-move-tree-start))
>              (org-defkey org-agenda-mode-map [C-mouse-4]
>               (quote org-agenda-earlier))
>              (org-defkey org-agenda-mode-map [C-mouse-5]
>               (quote org-agenda-later))
>              (org-defkey org-agenda-mode-map [drag-mouse-3]
>               (quote
>                (lambda (event) (interactive "e")
>                 (case (org-mouse-get-gesture event)
>                  (:left (org-agenda-earlier 1))
>                  (:right (org-agenda-later 1)))
>                 )
>                )
>               )
>              )
>             )
>  org-export-interblocks '((lob org-babel-exp-lob-one-liners)
>               (src org-babel-exp-inline-src-blocks))
>  org-occur-hook '(org-first-headline-recenter)
>  org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
>  org-confirm-babel-evaluate nil
>  org-infojs-options '((path . "http://bancs.bdx.com/chen/lib/org-info.js")
>               (view . "overview") (toc . "nil") (ftoc . "0")
>               (tdepth . "max") (sdepth . "max") (mouse . "underline")
>               (buttons . "0") (ltoc . "1") (up . :link-up)
>               (home . :link-home))
>  org-src-tab-acts-natively t
>  org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc
>                    org-beamer-auto-fragile-frames
>                    org-beamer-place-default-actions-for-lists)
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-export-blocks '((src org-babel-exp-src-block nil)
>              (comment org-export-blocks-format-comment t)
>              (ditaa org-export-blocks-format-ditaa nil)
>              (dot org-export-blocks-format-dot nil))
>  )
>
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/