* [babel] New handling of file output @ 2010-12-21 16:02 Dan Davison 2010-12-21 16:57 ` [babel] R: " Dan Davison 0 siblings, 1 reply; 5+ messages in thread From: Dan Davison @ 2010-12-21 16:02 UTC (permalink / raw) To: emacs-orgmode Please note the following changes to the way that org-babel handles file output. These may break existing org-babel files which use the :file header argument. :file <filename> should be understood as saying "write the result to <filename> and return a link to <filename>". This works for all languages. For graphics languages (e.g. ditaa, dot, gnuplot) there is no change in behavior: "result" in the above is the graphics, and a link to the image is placed in the org buffer. For general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell), the "result" written to file is the normal org-babel result (string, number, table). This is a backwards-incompatible change for R, which was previously interpreting :file to mean "send graphics to file". I will send a separate email concerning R. In order to return a file link from a src block without telling babel to save any results to that file, use :results <filename> and do not use :file. The code block can of course write arbitrary content to <filename>. Some examples: Save the output of ls -l as a .csv file (recall that :results value is the default): #+begin_src sh :file dirlisting.csv :sep , ls -l #+end_src Send the text output of ls -l directly to file: #+begin_src sh :results output :file dirlisting.txt ls -l #+end_src Dan ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [babel] R: New handling of file output 2010-12-21 16:02 [babel] New handling of file output Dan Davison @ 2010-12-21 16:57 ` Dan Davison 2011-01-01 21:49 ` Thomas S. Dye 2011-01-01 22:58 ` Thomas S. Dye 0 siblings, 2 replies; 5+ messages in thread From: Dan Davison @ 2010-12-21 16:57 UTC (permalink / raw) To: emacs-orgmode Dan Davison <dandavison7@gmail.com> writes: > Please note the following changes to the way that org-babel handles > file output. These may break existing org-babel files which use > the :file header argument. > > :file <filename> should be understood as saying "write the result > to <filename> and return a link to <filename>". > > This works for all languages. For graphics languages (e.g. ditaa, dot, > gnuplot) there is no change in behavior: "result" in the above is the > graphics, and a link to the image is placed in the org buffer. For > general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell), > the "result" written to file is the normal org-babel result (string, > number, table). > > This is a backwards-incompatible change for R, which was previously > interpreting :file to mean "send graphics to file". I will send a > separate email concerning R. Previously R understood :file <filename> to mean "save graphics to <filename>"[1]; now R behaves like other languages and sends the normal org-babel result to file (string, number, table). To tell R to save graphics[1] to file, use :results graphics. Some examples: Wrong! #+begin_src R :file img.png hist(rnorm(100)) "img.png is going to contain this string." #+end_src Use :results graphics save graphics: #+begin_src R :file img.png :results graphics hist(rnorm(100)) "But now img.png is going to contain graphics." #+end_src You may want to use `org-babel-default-header-args:R' to make this more convenient: #+begin_src emacs-lisp (setq org-babel-default-header-args:R '((:results . "graphics"))) #+end_src Alternatively the :results graphics header can be set in a property drawer for the subtree, or a #+babel: line, as usual. Now this will do what was intended #+begin_src R :file img.png hist(rnorm(100)) #+end_src Here is an example of saving something other than base graphics to file, and returning a link to the file. Note that :file is not used, and the filename must be returned. This could be used to save images created by non-base graphics libraries: #+begin_src R :results file :var file="savefile" write.something.to.file <- function(f) cat("hello", file=f) write.something.to.file(f=file) file #+end_src Dan * Footnotes [1] This only works for "base" graphics. > > In order to return a file link from a src block without telling babel > to save any results to that file, use :results <filename> and do not > use :file. The code block can of course write arbitrary content to > <filename>. > > Some examples: > > Save the output of ls -l as a .csv file (recall that :results value is > the default): > > #+begin_src sh :file dirlisting.csv :sep , > ls -l > #+end_src > > Send the text output of ls -l directly to file: > > #+begin_src sh :results output :file dirlisting.txt > ls -l > #+end_src > > Dan > > > _______________________________________________ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: Re: [babel] R: New handling of file output 2010-12-21 16:57 ` [babel] R: " Dan Davison @ 2011-01-01 21:49 ` Thomas S. Dye 2011-01-01 22:58 ` Thomas S. Dye 1 sibling, 0 replies; 5+ messages in thread From: Thomas S. Dye @ 2011-01-01 21:49 UTC (permalink / raw) To: Dan Davison; +Cc: emacs-orgmode Aloha all, Should :results graphic be documented in the :results header argument section of the Org-mode manual, or in the R-specific documentation? All the best, Tom On Dec 21, 2010, at 6:57 AM, Dan Davison wrote: > Dan Davison <dandavison7@gmail.com> writes: > >> Please note the following changes to the way that org-babel handles >> file output. These may break existing org-babel files which use >> the :file header argument. >> >> :file <filename> should be understood as saying "write the result >> to <filename> and return a link to <filename>". >> >> This works for all languages. For graphics languages (e.g. ditaa, >> dot, >> gnuplot) there is no change in behavior: "result" in the above is the >> graphics, and a link to the image is placed in the org buffer. For >> general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell), >> the "result" written to file is the normal org-babel result (string, >> number, table). >> >> This is a backwards-incompatible change for R, which was previously >> interpreting :file to mean "send graphics to file". I will send a >> separate email concerning R. > > Previously R understood :file <filename> to mean "save graphics to > <filename>"[1]; now R behaves like other languages and sends the > normal > org-babel result to file (string, number, table). To tell R to save > graphics[1] to file, use :results graphics. > > Some examples: > > Wrong! > > #+begin_src R :file img.png > hist(rnorm(100)) > "img.png is going to contain this string." > #+end_src > > Use :results graphics save graphics: > > #+begin_src R :file img.png :results graphics > hist(rnorm(100)) > "But now img.png is going to contain graphics." > #+end_src > > You may want to use `org-babel-default-header-args:R' to make this > more convenient: > > #+begin_src emacs-lisp > (setq org-babel-default-header-args:R > '((:results . "graphics"))) > #+end_src > > Alternatively the :results graphics header can be set in a property > drawer for the subtree, or a #+babel: line, as usual. > > Now this will do what was intended > #+begin_src R :file img.png > hist(rnorm(100)) > #+end_src > > Here is an example of saving something other than base graphics to > file, > and returning a link to the file. Note that :file is not used, and the > filename must be returned. This could be used to save images created > by > non-base graphics libraries: > > #+begin_src R :results file :var file="savefile" > write.something.to.file <- function(f) cat("hello", file=f) > write.something.to.file(f=file) > file > #+end_src > > > Dan > > > * Footnotes > [1] This only works for "base" graphics. > > > >> >> In order to return a file link from a src block without telling babel >> to save any results to that file, use :results <filename> and do not >> use :file. The code block can of course write arbitrary content to >> <filename>. >> >> Some examples: >> >> Save the output of ls -l as a .csv file (recall that :results value >> is >> the default): >> >> #+begin_src sh :file dirlisting.csv :sep , >> ls -l >> #+end_src >> >> Send the text output of ls -l directly to file: >> >> #+begin_src sh :results output :file dirlisting.txt >> ls -l >> #+end_src >> >> Dan >> >> >> _______________________________________________ >> Emacs-orgmode mailing list >> Please 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 > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: Re: [babel] R: New handling of file output 2010-12-21 16:57 ` [babel] R: " Dan Davison 2011-01-01 21:49 ` Thomas S. Dye @ 2011-01-01 22:58 ` Thomas S. Dye 2011-01-06 17:14 ` Dan Davison 1 sibling, 1 reply; 5+ messages in thread From: Thomas S. Dye @ 2011-01-01 22:58 UTC (permalink / raw) To: Dan Davison; +Cc: emacs-orgmode Aloha all, Here is an example of the new handling of file output with an R source code block that doesn't use "base" graphics: #+srcname: r-edge-angle-histogram #+begin_src R :results output graphics :var x=whole-adzes :file r/ adze_edge_angle.png :width 400 :height 300 library(ggplot2) adze.edge.angle <- ggplot(x, aes(edge_angle)) adze.edge.angle + geom_histogram(aes(y=..density..)) + geom_density(weight=2) + xlab("Measured cutting edge angle (degrees)") #+end_src #+results: [[file:r/adze_edge_angle.png]] Previously, the source line was: #+begin_src R :results output :var x=whole-adzes :file r/ adze_edge_angle.png :width 400 :height 300 The only change was to append graphics to :results output. All the best, Tom On Dec 21, 2010, at 6:57 AM, Dan Davison wrote: > Dan Davison <dandavison7@gmail.com> writes: > >> Please note the following changes to the way that org-babel handles >> file output. These may break existing org-babel files which use >> the :file header argument. >> >> :file <filename> should be understood as saying "write the result >> to <filename> and return a link to <filename>". >> >> This works for all languages. For graphics languages (e.g. ditaa, >> dot, >> gnuplot) there is no change in behavior: "result" in the above is the >> graphics, and a link to the image is placed in the org buffer. For >> general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell), >> the "result" written to file is the normal org-babel result (string, >> number, table). >> >> This is a backwards-incompatible change for R, which was previously >> interpreting :file to mean "send graphics to file". I will send a >> separate email concerning R. > > Previously R understood :file <filename> to mean "save graphics to > <filename>"[1]; now R behaves like other languages and sends the > normal > org-babel result to file (string, number, table). To tell R to save > graphics[1] to file, use :results graphics. > > Some examples: > > Wrong! > > #+begin_src R :file img.png > hist(rnorm(100)) > "img.png is going to contain this string." > #+end_src > > Use :results graphics save graphics: > > #+begin_src R :file img.png :results graphics > hist(rnorm(100)) > "But now img.png is going to contain graphics." > #+end_src > > You may want to use `org-babel-default-header-args:R' to make this > more convenient: > > #+begin_src emacs-lisp > (setq org-babel-default-header-args:R > '((:results . "graphics"))) > #+end_src > > Alternatively the :results graphics header can be set in a property > drawer for the subtree, or a #+babel: line, as usual. > > Now this will do what was intended > #+begin_src R :file img.png > hist(rnorm(100)) > #+end_src > > Here is an example of saving something other than base graphics to > file, > and returning a link to the file. Note that :file is not used, and the > filename must be returned. This could be used to save images created > by > non-base graphics libraries: > > #+begin_src R :results file :var file="savefile" > write.something.to.file <- function(f) cat("hello", file=f) > write.something.to.file(f=file) > file > #+end_src > > > Dan > > > * Footnotes > [1] This only works for "base" graphics. > > > >> >> In order to return a file link from a src block without telling babel >> to save any results to that file, use :results <filename> and do not >> use :file. The code block can of course write arbitrary content to >> <filename>. >> >> Some examples: >> >> Save the output of ls -l as a .csv file (recall that :results value >> is >> the default): >> >> #+begin_src sh :file dirlisting.csv :sep , >> ls -l >> #+end_src >> >> Send the text output of ls -l directly to file: >> >> #+begin_src sh :results output :file dirlisting.txt >> ls -l >> #+end_src >> >> Dan >> >> >> _______________________________________________ >> Emacs-orgmode mailing list >> Please 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 > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [babel] R: New handling of file output 2011-01-01 22:58 ` Thomas S. Dye @ 2011-01-06 17:14 ` Dan Davison 0 siblings, 0 replies; 5+ messages in thread From: Dan Davison @ 2011-01-06 17:14 UTC (permalink / raw) To: emacs-orgmode "Thomas S. Dye" <tsd@tsdye.com> writes: > Aloha all, > > Here is an example of the new handling of file output with an R source > code block that doesn't use "base" graphics: > > #+srcname: r-edge-angle-histogram > #+begin_src R :results output graphics :var x=whole-adzes :file r/ > adze_edge_angle.png :width 400 :height 300 > library(ggplot2) > adze.edge.angle <- ggplot(x, aes(edge_angle)) > adze.edge.angle + geom_histogram(aes(y=..density..)) + > geom_density(weight=2) + xlab("Measured cutting edge angle > (degrees)") > #+end_src I was initially a bit baffled by this example. If anyone else is curious as to why, when graphics are generated by ggplot2, :results output is required in addition to :results graphics, please see Erik Iverson's original post on producing grid-based (e.g. lattice, ggplot2) R graphics with org-babel (bearing in mind of course that the header arg syntax has changed as per this thread). http://article.gmane.org/gmane.emacs.orgmode/26082 Dan > > #+results: > [[file:r/adze_edge_angle.png]] > > Previously, the source line was: > #+begin_src R :results output :var x=whole-adzes :file r/ > adze_edge_angle.png :width 400 :height 300 > > The only change was to append graphics to :results output. > > All the best, > Tom > > On Dec 21, 2010, at 6:57 AM, Dan Davison wrote: > >> Dan Davison <dandavison7@gmail.com> writes: >> >>> Please note the following changes to the way that org-babel handles >>> file output. These may break existing org-babel files which use >>> the :file header argument. >>> >>> :file <filename> should be understood as saying "write the result >>> to <filename> and return a link to <filename>". >>> >>> This works for all languages. For graphics languages (e.g. ditaa, >>> dot, >>> gnuplot) there is no change in behavior: "result" in the above is the >>> graphics, and a link to the image is placed in the org buffer. For >>> general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell), >>> the "result" written to file is the normal org-babel result (string, >>> number, table). >>> >>> This is a backwards-incompatible change for R, which was previously >>> interpreting :file to mean "send graphics to file". I will send a >>> separate email concerning R. >> >> Previously R understood :file <filename> to mean "save graphics to >> <filename>"[1]; now R behaves like other languages and sends the >> normal >> org-babel result to file (string, number, table). To tell R to save >> graphics[1] to file, use :results graphics. >> >> Some examples: >> >> Wrong! >> >> #+begin_src R :file img.png >> hist(rnorm(100)) >> "img.png is going to contain this string." >> #+end_src >> >> Use :results graphics save graphics: >> >> #+begin_src R :file img.png :results graphics >> hist(rnorm(100)) >> "But now img.png is going to contain graphics." >> #+end_src >> >> You may want to use `org-babel-default-header-args:R' to make this >> more convenient: >> >> #+begin_src emacs-lisp >> (setq org-babel-default-header-args:R >> '((:results . "graphics"))) >> #+end_src >> >> Alternatively the :results graphics header can be set in a property >> drawer for the subtree, or a #+babel: line, as usual. >> >> Now this will do what was intended >> #+begin_src R :file img.png >> hist(rnorm(100)) >> #+end_src >> >> Here is an example of saving something other than base graphics to >> file, >> and returning a link to the file. Note that :file is not used, and the >> filename must be returned. This could be used to save images created >> by >> non-base graphics libraries: >> >> #+begin_src R :results file :var file="savefile" >> write.something.to.file <- function(f) cat("hello", file=f) >> write.something.to.file(f=file) >> file >> #+end_src >> >> >> Dan >> >> >> * Footnotes >> [1] This only works for "base" graphics. >> >> >> >>> >>> In order to return a file link from a src block without telling babel >>> to save any results to that file, use :results <filename> and do not >>> use :file. The code block can of course write arbitrary content to >>> <filename>. >>> >>> Some examples: >>> >>> Save the output of ls -l as a .csv file (recall that :results value >>> is >>> the default): >>> >>> #+begin_src sh :file dirlisting.csv :sep , >>> ls -l >>> #+end_src >>> >>> Send the text output of ls -l directly to file: >>> >>> #+begin_src sh :results output :file dirlisting.txt >>> ls -l >>> #+end_src >>> >>> Dan >>> >>> >>> _______________________________________________ >>> Emacs-orgmode mailing list >>> Please 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 >> Please 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 > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2011-01-06 17:14 UTC | newest] Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2010-12-21 16:02 [babel] New handling of file output Dan Davison 2010-12-21 16:57 ` [babel] R: " Dan Davison 2011-01-01 21:49 ` Thomas S. Dye 2011-01-01 22:58 ` Thomas S. Dye 2011-01-06 17:14 ` Dan Davison
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