From: Eric Schulte <schulte.eric@gmail.com>
To: Feiming Chen <feimingchen@yahoo.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5]
Date: Fri, 15 Jul 2011 08:32:00 -0600 [thread overview]
Message-ID: <87aacflflu.fsf@gmail.com> (raw)
In-Reply-To: 1310591651.9859.YahooMailClassic@web81704.mail.mud.yahoo.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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: test.org --]
[-- Type: text/x-org, Size: 700 bytes --]
#+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/
next prev parent reply other threads:[~2011-07-15 15:37 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-07-13 21:14 Bug: Org-Babel Mode R Plot Output to LaTeX File [Babel] [7.5] Feiming Chen
2011-07-15 14:32 ` Eric Schulte [this message]
2011-07-16 9:05 ` Stephen Eglen
2011-07-16 13:20 ` Eric Schulte
2011-07-16 18:54 ` Sebastien Vauban
2011-07-17 6:30 ` Bastien
-- strict thread matches above, loose matches on Subject: below --
2011-07-18 16:19 Feiming Chen
2011-07-18 16:36 ` Eric Schulte
2011-07-18 17:08 ` Feiming Chen
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