* Images from R in LaTeX and PDF
@ 2011-01-07 17:23 Ben Ward
2011-01-07 18:30 ` Thomas S. Dye
0 siblings, 1 reply; 6+ messages in thread
From: Ben Ward @ 2011-01-07 17:23 UTC (permalink / raw)
To: emacs-orgmode
Hi All,
I've been doing some work with babel and R to generate graphs that I've
then been including useing attr latex.
But when I include images the always appear very very small, even when I
mess about with the width settings of the attr latex line and remove the
options for wrap and such.
Does anybody else use R with images and org, and could tell me how they
handle including R graphics in their documents?
Thanks,
Ben. W
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: Images from R in LaTeX and PDF
2011-01-07 17:23 Images from R in LaTeX and PDF Ben Ward
@ 2011-01-07 18:30 ` Thomas S. Dye
2011-01-07 19:37 ` Ben Ward
0 siblings, 1 reply; 6+ messages in thread
From: Thomas S. Dye @ 2011-01-07 18:30 UTC (permalink / raw)
To: Ben Ward; +Cc: emacs-orgmode
Aloha Ben,
Can you share an example that doesn't work for you?
All the best,
Tom
On Jan 7, 2011, at 7:23 AM, Ben Ward wrote:
> Hi All,
>
> I've been doing some work with babel and R to generate graphs that
> I've then been including useing attr latex.
>
> But when I include images the always appear very very small, even
> when I mess about with the width settings of the attr latex line and
> remove the options for wrap and such.
>
> Does anybody else use R with images and org, and could tell me how
> they handle including R graphics in their documents?
>
> Thanks,
> Ben. W
>
> _______________________________________________
> 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] 6+ messages in thread
* Re: Images from R in LaTeX and PDF
2011-01-07 18:30 ` Thomas S. Dye
@ 2011-01-07 19:37 ` Ben Ward
2011-01-07 19:45 ` Erik Iverson
0 siblings, 1 reply; 6+ messages in thread
From: Ben Ward @ 2011-01-07 19:37 UTC (permalink / raw)
To: Thomas S. Dye; +Cc: emacs-orgmode
#+begin_src R :exports both
full <- read.csv(file="~/Documents/BSc Biology/Third Year/BY6001-40 -
Dissertation/Data and Analysis/Evolution Results.csv", head=T)
library("lattice")
ecoli = subset(full, Bacterium=="E.coli")
edett = subset(ecoli, Cleaner=="Dettol")
egarl = subset(ecoli, Cleaner=="Garlic")
MIC.mod = lm(MIC. ~ 1+Challenge*Cleaner*Replicate, data=ecoli)
#+end_src
#+begin_src R :file fig1.pdf
xyplot( MIC.+fitted(MIC.mod) ~ Challenge, data=ecoli,
xlab="Challenge", ylab="MIC %", auto.key=TRUE)
#+end_src
#+attr_latex: width=0.6\textwidth wrap placement={h}{0.4\textwidth}
#+label: fig:one
#+caption: Linar Plot of real data and fitted model values
#+results: fig1
[[file:fig1.pdf]]
In the case of this code, actually altering size works, but it keeps
putting the image at the end of my document. Then other images, placed
with pretty much the same code, give or take for filenames and such,
won't increace in size, but will alter their movement.
I'm wondering if using pure latex for my images would be an easier solution.
Cheers,
Ben.
On 07/01/2011 18:30, Thomas S. Dye wrote:
> Aloha Ben,
>
> Can you share an example that doesn't work for you?
>
> All the best,
> Tom
>
> On Jan 7, 2011, at 7:23 AM, Ben Ward wrote:
>
>> Hi All,
>>
>> I've been doing some work with babel and R to generate graphs that
>> I've then been including useing attr latex.
>>
>> But when I include images the always appear very very small, even
>> when I mess about with the width settings of the attr latex line and
>> remove the options for wrap and such.
>>
>> Does anybody else use R with images and org, and could tell me how
>> they handle including R graphics in their documents?
>>
>> Thanks,
>> Ben. W
>>
>> _______________________________________________
>> 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] 6+ messages in thread
* Re: Images from R in LaTeX and PDF
2011-01-07 19:37 ` Ben Ward
@ 2011-01-07 19:45 ` Erik Iverson
2011-01-07 19:50 ` Ben Ward
0 siblings, 1 reply; 6+ messages in thread
From: Erik Iverson @ 2011-01-07 19:45 UTC (permalink / raw)
To: Ben Ward; +Cc: emacs-orgmode
And what version of org are you using?
Ben Ward wrote:
>
> #+begin_src R :exports both
> full <- read.csv(file="~/Documents/BSc Biology/Third Year/BY6001-40 -
> Dissertation/Data and Analysis/Evolution Results.csv", head=T)
> library("lattice")
> ecoli = subset(full, Bacterium=="E.coli")
> edett = subset(ecoli, Cleaner=="Dettol")
> egarl = subset(ecoli, Cleaner=="Garlic")
> MIC.mod = lm(MIC. ~ 1+Challenge*Cleaner*Replicate, data=ecoli)
> #+end_src
>
> #+begin_src R :file fig1.pdf
> xyplot( MIC.+fitted(MIC.mod) ~ Challenge, data=ecoli, xlab="Challenge",
> ylab="MIC %", auto.key=TRUE)
> #+end_src
>
> #+attr_latex: width=0.6\textwidth wrap placement={h}{0.4\textwidth}
> #+label: fig:one
> #+caption: Linar Plot of real data and fitted model values
> #+results: fig1
> [[file:fig1.pdf]]
>
> In the case of this code, actually altering size works, but it keeps
> putting the image at the end of my document. Then other images, placed
> with pretty much the same code, give or take for filenames and such,
> won't increace in size, but will alter their movement.
> I'm wondering if using pure latex for my images would be an easier
> solution.
>
> Cheers,
> Ben.
>
>
> On 07/01/2011 18:30, Thomas S. Dye wrote:
>> Aloha Ben,
>>
>> Can you share an example that doesn't work for you?
>>
>> All the best,
>> Tom
>>
>> On Jan 7, 2011, at 7:23 AM, Ben Ward wrote:
>>
>>> Hi All,
>>>
>>> I've been doing some work with babel and R to generate graphs that
>>> I've then been including useing attr latex.
>>>
>>> But when I include images the always appear very very small, even
>>> when I mess about with the width settings of the attr latex line and
>>> remove the options for wrap and such.
>>>
>>> Does anybody else use R with images and org, and could tell me how
>>> they handle including R graphics in their documents?
>>>
>>> Thanks,
>>> Ben. W
>>>
>>> _______________________________________________
>>> 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] 6+ messages in thread
* Re: Images from R in LaTeX and PDF
2011-01-07 19:45 ` Erik Iverson
@ 2011-01-07 19:50 ` Ben Ward
0 siblings, 0 replies; 6+ messages in thread
From: Ben Ward @ 2011-01-07 19:50 UTC (permalink / raw)
To: Erik Iverson; +Cc: emacs-orgmode
I'm using 7.4, which I think (unless a new versions recently arisen),
the latest one, as it was recommended for interacting with R through babel.
Thanks,
Ben W.
On 07/01/2011 19:45, Erik Iverson wrote:
> And what version of org are you using?
>
> Ben Ward wrote:
>>
>> #+begin_src R :exports both
>> full <- read.csv(file="~/Documents/BSc Biology/Third Year/BY6001-40
>> - Dissertation/Data and Analysis/Evolution Results.csv", head=T)
>> library("lattice")
>> ecoli = subset(full, Bacterium=="E.coli")
>> edett = subset(ecoli, Cleaner=="Dettol")
>> egarl = subset(ecoli, Cleaner=="Garlic")
>> MIC.mod = lm(MIC. ~ 1+Challenge*Cleaner*Replicate, data=ecoli)
>> #+end_src
>>
>> #+begin_src R :file fig1.pdf
>> xyplot( MIC.+fitted(MIC.mod) ~ Challenge, data=ecoli,
>> xlab="Challenge", ylab="MIC %", auto.key=TRUE)
>> #+end_src
>>
>> #+attr_latex: width=0.6\textwidth wrap placement={h}{0.4\textwidth}
>> #+label: fig:one
>> #+caption: Linar Plot of real data and fitted model values
>> #+results: fig1
>> [[file:fig1.pdf]]
>>
>> In the case of this code, actually altering size works, but it keeps
>> putting the image at the end of my document. Then other images,
>> placed with pretty much the same code, give or take for filenames and
>> such, won't increace in size, but will alter their movement.
>> I'm wondering if using pure latex for my images would be an easier
>> solution.
>>
>> Cheers,
>> Ben.
>>
>>
>> On 07/01/2011 18:30, Thomas S. Dye wrote:
>>> Aloha Ben,
>>>
>>> Can you share an example that doesn't work for you?
>>>
>>> All the best,
>>> Tom
>>>
>>> On Jan 7, 2011, at 7:23 AM, Ben Ward wrote:
>>>
>>>> Hi All,
>>>>
>>>> I've been doing some work with babel and R to generate graphs that
>>>> I've then been including useing attr latex.
>>>>
>>>> But when I include images the always appear very very small, even
>>>> when I mess about with the width settings of the attr latex line
>>>> and remove the options for wrap and such.
>>>>
>>>> Does anybody else use R with images and org, and could tell me how
>>>> they handle including R graphics in their documents?
>>>>
>>>> Thanks,
>>>> Ben. W
>>>>
>>>> _______________________________________________
>>>> 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] 6+ messages in thread
* Re: Images from R in LaTeX and PDF
@ 2011-01-08 12:28 Dan Davison
0 siblings, 0 replies; 6+ messages in thread
From: Dan Davison @ 2011-01-08 12:28 UTC (permalink / raw)
To: benjamin.ward; +Cc: emacs-orgmode
Ben Ward <benjamin.ward@bathspa.org> writes:
> #+begin_src R :exports both
> full <- read.csv(file="~/Documents/BSc Biology/Third Year/BY6001-40 -
> Dissertation/Data and Analysis/Evolution Results.csv", head=T)
> library("lattice")
> ecoli = subset(full, Bacterium=="E.coli")
> edett = subset(ecoli, Cleaner=="Dettol")
> egarl = subset(ecoli, Cleaner=="Garlic")
> MIC.mod = lm(MIC. ~ 1+Challenge*Cleaner*Replicate, data=ecoli)
> #+end_src
Hi Ben,
Use the :width and :height header args to alter the dimensions of the
graphics. The arguments go straight through to the R device, so if you
are plotting to pdf they will be interpreted as inches (whereas they
will be pixels for png, jpeg etc).
With current Org, you will also need :results graphics in order to tell
R to send graphics to the designated file.
In addition, with lattice graphics, unless you are using :session, I
believe you will need :results output (so :results output graphics).
Do get back to us with any problems. There are several people who
routinely use R to include graphics in Org documents.
Dan
p.s. Request to everyone: can we try as much as possible to use
reproducible examples on-list? I.e. toy examples that anyone can
execute, instead of real examples that rely on datasets that not
everyone has access to.
> #+begin_src R :file fig1.pdf
> xyplot( MIC.+fitted(MIC.mod) ~ Challenge, data=ecoli,
> xlab="Challenge", ylab="MIC %", auto.key=TRUE)
> #+end_src
>
> #+attr_latex: width=0.6\textwidth wrap placement={h}{0.4\textwidth}
> #+label: fig:one
> #+caption: Linar Plot of real data and fitted model values
> #+results: fig1
> [[file:fig1.pdf]]
>
> In the case of this code, actually altering size works, but it keeps
> putting the image at the end of my document. Then other images, placed
> with pretty much the same code, give or take for filenames and such,
> won't increace in size, but will alter their movement.
> I'm wondering if using pure latex for my images would be an easier solution.
>
> Cheers,
> Ben.
>
>
> On 07/01/2011 18:30, Thomas S. Dye wrote:
>> Aloha Ben,
>>
>> Can you share an example that doesn't work for you?
>>
>> All the best,
>> Tom
>>
>> On Jan 7, 2011, at 7:23 AM, Ben Ward wrote:
>>
>>> Hi All,
>>>
>>> I've been doing some work with babel and R to generate graphs that
>>> I've then been including useing attr latex.
>>>
>>> But when I include images the always appear very very small, even
>>> when I mess about with the width settings of the attr latex line and
>>> remove the options for wrap and such.
>>>
>>> Does anybody else use R with images and org, and could tell me how
>>> they handle including R graphics in their documents?
>>>
>>> Thanks,
>>> Ben. W
>>>
>>> _______________________________________________
>>> 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] 6+ messages in thread
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2011-01-07 17:23 Images from R in LaTeX and PDF Ben Ward
2011-01-07 18:30 ` Thomas S. Dye
2011-01-07 19:37 ` Ben Ward
2011-01-07 19:45 ` Erik Iverson
2011-01-07 19:50 ` Ben Ward
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2011-01-08 12:28 Dan Davison
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