Re: [R] help with cube3d cube size

From: Mark Kimpel <mwkimpel_at_gmail.com>
Date: Thu, 26 Jun 2008 12:07:40 -0400

Duncan & Ben,

Thanks for giving me some tips as to how I can best investigate packages. I"ve been using ESS-Emacs and the help pages are HTML. Looks like I need to figure out how to enable HTML help.

As for a draft vignette, sure, I would be happy (and honored) to contribute as best I can. I would need a lot of help from the two of you, but it would be a good learning experience for me and give me a chance to give something back to the community which has been so good to me.

Speaking of vignettes, I wonder if there should be a vignette written called "navigating new functions and packages for the R beginner" or be included as a chapter in "An Introduction to R", which focuses on R-base functionality. I"m just musing here, but I often think that if I need to learn something perhaps others do too.

One thing at a time, however, so I'll work on a draft and send it to you for comments and input. Ben, if you get such a list of packages with functions that depend on rgl, send it to me.

Mark

On Thu, Jun 26, 2008 at 7:02 AM, Duncan Murdoch <murdoch_at_stats.uwo.ca> wrote:
> Mark Kimpel wrote:
>>
>> Thanks for the pointers. I think the package is great, just want to
>> use it to its full potential without driving the list crazy with
>> questions. Below is my output to help and sessionInfo(). I don't see
>> the scaling functions, although I now see that they can be retrieved
>> with ?matrices. You guys are the experts as to what should go where,
>> but for someone unfamiliar with how rgl works, having them print out
>> with help(package = "rgl") would make some of these functions more
>> obvious to the newbie. Mark
>>
>
> The issue here is that several of those are documented on the same page, and
> that index lists the names of help pages, not all of the aliases that point
> there. The index in the HTML help version (or the CHM help in Windows)
> repeats each alias, so you'll see things like
>
> scale3d Work with homogeneous coordinates
> scaleMatrix Work with homogeneous coordinates
>
> as well as the entry for matrices as below. I can see arguments for both:
> repetition is bad, full coverage is good. The index in the pdf document is
> another approach: it lists all the aliases, and tells you which topic
> documents them.
>
> All of this is common to all R packages; rgl isn't doing anything special to
> produce these lists.
>
> Duncan Murdoch
>>
>> aspect3d Set the aspect ratios of the current plot
>> axes3d Draw boxes, axes and other text outside the
>> data
>> ellipse3d Make an ellipsoid
>> grid3d Add a grid to a 3D plot
>> matrices Work with homogeneous coordinates
>> par3d Set or Query RGL Parameters
>> par3dinterp Interpolator for par3d parameters
>> persp3d Surface plots
>> play3d Play animation of rgl scene
>> plot3d 3D Scatterplot
>> points3d add primitive set shape
>> qmesh3d 3D Quadrangle Mesh objects
>> r3d Generic 3D interface
>> rgl-package 3D visualization device system
>> rgl.bbox Set up Bounding Box decoration
>> rgl.bg Set up Background
>> rgl.bringtotop Assign focus to an RGL window
>> rgl.clear scene management
>> rgl.light add light source
>> rgl.material Generic Appearance setup
>> rgl.postscript export screenshot
>> rgl.primitive add primitive set shape
>> rgl.setMouseCallbacks User callbacks on mouse events
>> rgl.snapshot export screenshot
>> rgl.spheres add sphere set shape
>> rgl.surface add height-field surface shape
>> rgl.texts add text
>> rgl.user2window Convert between rgl user and window coordinates
>> rgl.viewpoint Set up viewpoint
>> select3d Select a rectangle in an RGL scene
>> spin3d Create a function to spin a scene at a fixed
>> rate
>> sprites3d add sprite set shape
>> subdivision3d generic subdivision surface method
>> surface3d add height-field surface shape
>>
>>
>>
>>>
>>> sessionInfo()
>>>
>>
>> R version 2.7.1 (2008-06-23)
>> i686-pc-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] rgl_0.79 graph_1.18.1
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.11 tools_2.7.1
>>
>> On Wed, Jun 25, 2008 at 5:25 PM, Duncan Murdoch <murdoch_at_stats.uwo.ca>
>> wrote:
>>
>>>
>>> Mark Kimpel wrote:
>>>
>>>>
>>>> Ben and Duncan,
>>>>
>>>> Thanks for your helpful suggestions. I"m having some difficulty
>>>> navigating this really good package using my normal learning
>>>> techniques. When I do 'help(package = "rgl") it seems only a very
>>>> small subset of functions available show up.
>>>>
>>>
>>> I think the full list shows up there, if you're using a current version.
>>> What specific function is missing?
>>>
>>>>
>>>> Perusing the rgl.pdf
>>>> downloaded from CRAN demonstrates the same lack of documentation.
>>>>
>>>>
>>>
>>> All of the functions intended for users are documented, and they show up
>>> in
>>> rgl.pdf.
>>>
>>>>
>>>> There is no vignette. In addition, I have found at least one other
>>>> package with 3d functions (emdbook::curve3d()).
>>>>
>>>>
>>>
>>> A vignette would be nice, but there isn't one. Our paper from useR 2007
>>> is
>>> the most recent reference (see
>>>
>>> http://www.r-project.org/conferences/useR-2007/program/presentations/murdoch.pdf);
>>> it cites Daniel's 2003 thesis and the 2003 paper about the package.
>>> After those, the NEWS file lists some recent additions.
>>>
>>> emdbook makes use of rgl and some other 3d engines, as does misc3d.
>>> scatterplot3d does it's own drawing. rggobi is a completely different
>>> interactive package.
>>>
>>>>
>>>> What is the best resource for learning about all the foo3d() and lower
>>>> level functionality that rgl and its dependents provide? I saw a book
>>>> at B&N just last week on openGL. Would that be helpful?
>>>>
>>>>
>>>
>>> It might, but probably not. rgl is intended to be a higher level R-style
>>> interface to the things described in a book like that. So if you have a
>>> particular question about how to do something, you'd never find it there.
>>> On the other hand, if you want to know if something is possible, then
>>> that
>>> might be a place to look for ideas.
>>>
>>> Duncan Murdoch
>>>
>>>>
>>>> Mark
>>>>
>>>> On Tue, Jun 24, 2008 at 10:54 PM, Ben Bolker <bolker_at_ufl.edu> wrote:
>>>>
>>>>
>>>>>
>>>>> Mark Kimpel <mwkimpel <at> gmail.com> writes:
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> I'm using the command below on an open3d() object to create a shaded
>>>>>> cube. Changes to myScalingFactor do not effect changes in the size of
>>>>>> the cube. What is the correct approach? Mark
>>>>>>
>>>>>>
>>>>>
>>>>> how about scale3d() ?
>>>>>
>>>>> shade3d(translate3d(scale3d(cube3d(),5,5,5),-6,1,-1),col="blue", alpha
>>>>> =
>>>>> 0.2)
>>>>> shade3d(translate3d(cube3d(),-6,1,-1),col="green", alpha = 0.2)
>>>>> shade3d(translate3d(scale3d(cube3d(),10,10,10),-6,1,-1),col="red",
>>>>> alpha
>>>>> = 0.2)
>>>>>
>>>>> ______________________________________________
>>>>> R-help_at_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.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

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