Re: [R] Figures within tables [slightly off-topic]
On 04/13/2010 06:07 AM, Peter Jepsen wrote: Dear R-listers I am writing a manuscript for a scientific journal in clinical medicine. I have three groups of patients, and I present a 10*3 table of their characteristics in Table 1. Some of their characteristics, e.g. their age, are on a continuous scale, others are dichotomous. I am thinking of presenting the age distribution in each group as miniature graphs, each of which must fit in one table cell. I am hoping that someone can answer these questions: 1. Has anybody ever seen something like this published anywhere? 2. Should I draw the entire table as a figure, or should I make a table in Word (or similar) and manually insert the graphs in their cells? 3. Are there R packages that can draw tables? 4. And one for you editors out there: Would such a table count as one figure, several figures, or a table?! Forgive me for being somewhat off-topic. I hope for your help anyway. Hi Peter, This sounds like Edward Tufte's sparklines and I think there was a discussion of this sort of graphic a couple of years ago. Yep, see: http://finzi.psych.upenn.edu/R/Rhelp02/archive/76508.html Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Figures within tables [slightly off-topic]
On 13-Apr-10 09:54:20, Jim Lemon wrote: On 04/13/2010 06:07 AM, Peter Jepsen wrote: Dear R-listers I am writing a manuscript for a scientific journal in clinical medicine. I have three groups of patients, and I present a 10*3 table of their characteristics in Table 1. Some of their characteristics, e.g. their age, are on a continuous scale, others are dichotomous. I am thinking of presenting the age distribution in each group as miniature graphs, each of which must fit in one table cell. I am hoping that someone can answer these questions: 1. Has anybody ever seen something like this published anywhere? 2. Should I draw the entire table as a figure, or should I make a table in Word (or similar) and manually insert the graphs in their cells? 3. Are there R packages that can draw tables? 4. And one for you editors out there: Would such a table count as one figure, several figures, or a table?! Forgive me for being somewhat off-topic. I hope for your help anyway. Hi Peter, This sounds like Edward Tufte's sparklines and I think there was a discussion of this sort of graphic a couple of years ago. Yep, see: http://finzi.psych.upenn.edu/R/Rhelp02/archive/76508.html Jim It does indeed sound like sparklines! In the posting by Robin Hankin that Jim refers to, the URL for Tufte's illustration of sparklines is: http://www.edwardtufte.com/bboard/ q-and-a-fetch-msg?msg_id=0001ORtopic_id=1 [equivalently: http://tinyurl.com/6bbkw ] Robin posted that he would send privately to the original poster examples of how to do it in Sweave. It could be useful if Robin could provide a pointer to on-line examples of such usage. In general, the key to getting that sort of thing right is to prepare the graphic beforehand as an Encapsulated PostScript (EPS) file, which R can do very nicely. This can then be imported into document-preparation software which can handle EPS files properly. LaTeX can do that, also the classic groff (always present on Linux systems). Maybe Word can, but don't ask me about that; however, if you live in that world then R should be able to produce Windows Metafiles (WMF) of graphics which could then be imported. The point here is that an EPS file contains a %%BoundingBox line which states what the dimensions of the graphic are in terms of the within-file coordinate system (specifically, location of lower left and upper right corners). The important thing about that is that the software which produces the EPS file should compute a good BoundingBox -- if that is wrong, then the result can be awful. R is good at that, though you may need to tweak things using relevant options in the postscript() command. You may even need to explicitly edit the %%BoundingBox line in the EPS file to get it exactly as you want it! Once that is available, the document software will alow you to specify somehow the dimensions of the graphic as it will appear in the text. I'm no expert on LaTeX, so can't discuss details of this. Maybe other will; maybe Robin's examples will explain. In groff, however, you can specify these directly, or indirectly via a macro, and then import the graphic where you want; and you can even define a special character which will display as the graphic and will also have the same status as any ther character (e.g. the letter A) and be automatically placed, and scaled according to the current text point size, just like an ordinary text character. Either way, there is no problem putting a graphic into a cell in a table. As it happens, I received via the groff mailing-list a few months ago a query from someone who precisely wanted to implement Tufte sparklines in running text. He provided and example of text and of a sparkline graphic. I was then able to create an example of how this works in groff. He gave permission for his example and the graphic to be used in communicating the method communicated to others, so I have placed on my website A: An explanation of how it is done, with illustrations using his EPS graphic: http://www.zen89632.zen.co.uk/Misc/do_spark_howto.pdf B: The example EPS file he provided: http://www.zen89632.zen.co.uk/Misc/spark.average.fund.size.eps Note that, owing to peculiarites of the graphic (in particular rthe X-axis) it does not render well in the PDF file -- you may need to zoom to 200% to see it properly. This is an example of importing an EPS file into running text, with adjustable vertical and horizontal dimensions, in other words a true Tufte sparkline. Hoping this helps, at least for explanation! As to what editors may think of it -- Is it text? Is it graphics? Is it a table? I just don't know. They tick their own boxes. It is certainly playing the *rôle* of text, but the fact that there needs to be a graphics (e.g. EPS) file present in order for it to work means that their graphics light may flash red. And in your application it is certainly occurring in the context of a table. I'd go for table myself (with
[R] Figures within tables [slightly off-topic]
Dear R-listers I am writing a manuscript for a scientific journal in clinical medicine. I have three groups of patients, and I present a 10*3 table of their characteristics in Table 1. Some of their characteristics, e.g. their age, are on a continuous scale, others are dichotomous. I am thinking of presenting the age distribution in each group as miniature graphs, each of which must fit in one table cell. I am hoping that someone can answer these questions: 1. Has anybody ever seen something like this published anywhere? 2. Should I draw the entire table as a figure, or should I make a table in Word (or similar) and manually insert the graphs in their cells? 3. Are there R packages that can draw tables? 4. And one for you editors out there: Would such a table count as one figure, several figures, or a table?! Forgive me for being somewhat off-topic. I hope for your help anyway. Best regards, Peter. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Figures within tables [slightly off-topic]
Hello, I am writing a manuscript for a scientific journal in clinical medicine. I have three groups of patients, and I present a 10*3 table of their characteristics in Table 1. Some of their characteristics, e.g. their age, are on a continuous scale, others are dichotomous. I am thinking of presenting the age distribution in each group as miniature graphs, each of which must fit in one table cell. I am hoping that someone can answer these questions: 1. Has anybody ever seen something like this published anywhere? 2. Should I draw the entire table as a figure, or should I make a table in Word (or similar) and manually insert the graphs in their cells? Depending on your needs, there's another solution. You could output LaTeX, and compile that to a PDF. The first thing I thought of when I read your topic was the describe function in Hmisc. The help file for ?describe references http://biostat.mc.vanderbilt.edu/twiki/pub/Main/Hmisc/counties.pdf Probably not exactly what you're looking for, but it might be start. See also: http://texblog.wordpress.com/2008/02/04/placing-graphicsimages-inside-a-table/ I would probably go this route, generating code to produce a LaTeX table and the associated image files. I've also used low-level grid graphics function calls (e.g., grid.text ) to produce 'tables' with hazard ratio type graphics included as a column. (a 'forest plot'). Hope that helps, Erik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Figures within tables [slightly off-topic]
Hi, On 12 April 2010 22:07, Peter Jepsen p...@dce.au.dk wrote: 3. Are there R packages that can draw tables? the gplots package has a textplot() function, and the gridExtra package a tableGrob(), http://rwiki.sciviews.org/doku.php?id=tips:graphics-grid:table In theory it should be possible to adapt the latter to allow the placement of a (preferably lattice / ggplot2 / Grid) graphic in the desired cells. HTH, baptiste __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
