[R] 3-D response surface using wireframe()
David Winsemius
dwinsemius at comcast.net
Fri Apr 9 21:48:21 CEST 2010
I do not think the mail server accepts .jpg formats which was the
format in which I got your attachment the first time (because of your
having copied me directly.) I don't see much need to send a pdf
because the code you offered does work and the data made it through
(because .txt and .pdf are types that the mailserver accepts.)
Back in 2007 Sarkar suggested that it would be possible to project
grids on the walls of the bounding box but since the original poster
did not reply, it appears Sarkar did not deliver a worked solution.
http://finzi.psych.upenn.edu/R/Rhelp02/archive/95759.html
And then in 2008 he referred the questioner to the section of the
Lattice examples I earlier cited:
http://finzi.psych.upenn.edu/Rhelp10/2008-October/176466.html
--
David.
On Apr 9, 2010, at 3:27 PM, array chip wrote:
> Sorry the example plot didn't go through last time, here it is:
>
> Thanks
>
> John
>
> --- On Fri, 4/9/10, array chip <arrayprofile at yahoo.com> wrote:
>
>> From: array chip <arrayprofile at yahoo.com>
>> Subject: Re: [R] 3-D response surface using wireframe()
>> To: "David Winsemius" <dwinsemius at comcast.net>, "Felix Andrews" <felix at nfrac.org
>> >
>> Cc: r-help at r-project.org
>> Date: Friday, April 9, 2010, 1:09 PM
>> Hi David and Felix,
>>
>> Thank you very much for your suggestions. To be honest,
>> this has become beyond my understanding of lattice plots
>> now. I am relatively new to lattice plots, so have no idea
>> how function within function works (for example, how does
>> panel.3dpolygon() within panel.3d.wireframe() within
>> wirefarme() works, totally have no clue.
>>
>> Felix, your example code of panel.3dpolygon() for volcano
>> plot does what I want, but again, I don't know how to tweak
>> your example to suit my case.
>>
>> I attached an example dataset, and an example of the plot
>> that I wanted to make (especially those grid lines on the 3
>> bounding surfaces of the box, and if possible remove those
>> front edges of the box to make it look like open).
>>
>> dat<-read.table("dat.txt",sep='\t',header=T,row.names=1)
>>
>> library(lattice)
>> wireframe(z ~ x*y, data = dat,
>> scales = list(arrows = FALSE, cex=0.9, col="black",font=3,
>> tick.number=6, z=list(tick.number=10,
>> tck
>> =
>> 0.8
>> ,distance
>> =0.8),x=list(tck=0.8,distance=0.6),y=list(tck=0.7,distance=0.6)),
>> zlim=seq(-14,4,by=2),
>> zlab=list(label="Z", rot=90,cex=0.9),
>> xlab=list(label="X", rot=15.5),
>> ylab=list(label="Y", rot=-33),
>> drape = T,
>> at=seq(min(dat$z),max(dat$z),length=50),
>> col.regions=rgb(colorRamp(c("white", "red"))(seq(0, 1,
>> length = 50)), max = 255),
>> colorkey = F,
>> par.box=list(lwd=2), ## line width of box
>> screen = list(z = 210, x = -75, y = 5),
>> scpos=list(x=9,y=5,z=2) ## where axes are draw
>> )
>>
>> Thank you all very much for the help. It's fun to learn.
>>
>> John
>>
>> --- On Thu, 4/8/10, Felix Andrews <felix at nfrac.org>
>> wrote:
>>
>>> From: Felix Andrews <felix at nfrac.org>
>>> Subject: Re: [R] 3-D response surface using
>> wireframe()
>>> To: "David Winsemius" <dwinsemius at comcast.net>
>>> Cc: "array chip" <arrayprofile at yahoo.com>,
>> r-help at r-project.org
>>> Date: Thursday, April 8, 2010, 9:56 PM
>>> On 9 April 2010 11:18, David
>>> Winsemius <dwinsemius at comcast.net>
>>> wrote:
>>>> On Apr 8, 2010, at 8:29 PM, array chip wrote:
>>>>
>>>>> David,
>>>>>
>>>>> Thansk again! Sarkar's Lattice book is
>> excellent
>>> source for lattice. Here
>>>>> is a link for all the figures and codes used
>> in
>>> the book. You example is
>>>>> figure 13.7.
>>>>>
>>>>> http://lmdvr.r-forge.r-project.org/figures/figures.html
>>>>>
>>>>> I got the first point! For the second point
>> below,
>>> Figure 13.7 an
>>>>> excellent example for projecting the 3D
>> dataset
>>> onto the bounding surface,
>>>>> but it's not what I meant. I think I didn't
>>> explain what I wanted clearly.
>>>>> What I really wanted is a simple straight
>> grid
>>> lines across the tick marks
>>>>> for 3 bounding surfaces of the box, not a
>>> projection of the 3D dataset. Hope
>>>>> I have explained clearly this time.
>>>>
>>>> You have not convinced me that I misunderstood
>> what
>>> you wanted. I figured
>>>> that you would use something other than
>> transforming
>>> the data driven contour
>>>> lines. But if you want to use a lattice function
>> there
>>> is a panel.grid, but
>>>> I still suspect it will need to be 3dto3d
>> transformed
>>> onto one of the "lim"
>>>> extremes.
>>>
>>> Might be a little easier to use panel.3dpolygon from
>>> latticeExtra.
>>> (or not)
>>> e.g. something like
>>>
>>> wireframe(volcano, drape = TRUE, scales = list(arrows
>> =
>>> FALSE),
>>> panel.3d.wireframe = function(x,y,z,...) {
>>> panel.3dwire(x,y,z,...)
>>> panel.3dpolygon(x = rep(pretty(x), each = 3),
>>> y = min(y), z =
>>> c(range(z),NA),
>>>
>>> ..., border="grey", lwd=2)
>>> })
>>>
>>>
>>>>
>>>>>
>>>>> Many thanks
>>>>>
>>>>> John
>>>>>
>>>>>
>>>>> --- On Thu, 4/8/10, David Winsemius <dwinsemius at comcast.net>
>>> wrote:
>>>>>
>>>>>> From: David Winsemius <dwinsemius at comcast.net>
>>>>>> Subject: Re: [R] 3-D response surface
>> using
>>> wireframe()
>>>>>> To: "array chip" <arrayprofile at yahoo.com>
>>>>>> Cc: r-help at r-project.org
>>>>>> Date: Thursday, April 8, 2010, 3:46 PM
>>>>>>
>>>>>> On Apr 8, 2010, at 3:13 PM, array chip
>> wrote:
>>>>>>
>>>>>>> David,
>>>>>>>
>>>>>>> That does the job! Thanks a lot.
>>>>>>>
>>>>>>> Now I am very very close to what I
>> want.
>>> Still have a
>>>>>>
>>>>>> couple of
>>>>>>>
>>>>>>> small adjustments to make.
>>>>>>>
>>>>>>> 1. I use drape=TRUE to draw grid and
>> color
>>> on the
>>>>>>
>>>>>> surface, is there
>>>>>>>
>>>>>>> a parameter to adjust the density of
>> the
>>> grid?
>>>>>>
>>>>>> If you mean the spacing between points,
>> then
>>> isn't that
>>>>>> determined by
>>>>>> the density of the gridded data
>> arguments
>>> before they get
>>>>>> to the
>>>>>> wireframe function?
>>>>>>
>>>>>>>
>>>>>>> 2. Is there a way that I can add grid
>> to
>>> the axis
>>>>>>
>>>>>> surface? I mean
>>>>>>>
>>>>>>> the sides of the box, between x &
>> y,
>>> between x
>>>>>>
>>>>>> & z, and between y &
>>>>>>>
>>>>>>> z? And I need to choose which 3 side
>> of
>>> the box that I
>>>>>>
>>>>>> want to add
>>>>>>>
>>>>>>> grid?
>>>>>>
>>>>>> See Figure 13.7 of Sarkar's Lattice text
>> for
>>> an example of
>>>>>> a panel
>>>>>> function that collapses the contourLines
>> of
>>> the volcano
>>>>>> dataset at the
>>>>>> top bounding surface by using
>> ltransform3dto3d
>>> with a z
>>>>>> argument of
>>>>>> zlim.scaled[2]. I would think that a
>> grid
>>> could be 3dto3d
>>>>>> transformed
>>>>>> similarly.
>>>>>>
>>>>>> --
>>>>>> David.
>>>>>>
>>>>>>>
>>>>>>> Thank you all for the help. It's fun
>> to
>>> play with
>>>>>>
>>>>>> wireframe
>>>>>>>
>>>>>>> John
>>>>>>>
>>>>>>> --- On Wed, 4/7/10, David Winsemius
>> <dwinsemius at comcast.net>
>>>>>>
>>>>>> wrote:
>>>>>>>
>>>>>>>> From: David Winsemius <dwinsemius at comcast.net>
>>>>>>>> Subject: Re: [R] 3-D response
>> surface
>>> using
>>>>>>
>>>>>> wireframe()
>>>>>>>>
>>>>>>>> To: "array chip" <arrayprofile at yahoo.com>
>>>>>>>> Cc: r-help at r-project.org
>>>>>>>> Date: Wednesday, April 7, 2010,
>> 9:22
>>> PM
>>>>>>>>
>>>>>>>> On Apr 7, 2010, at 8:58 PM, array
>> chip
>>> wrote:
>>>>>>>>
>>>>>>>>> With the help document, i
>> finally
>>> find a set
>>>>>>
>>>>>> of values
>>>>>>>>
>>>>>>>> of for x=,y=
>>>>>>>>>
>>>>>>>>> and z= in "screen" argument
>> that
>>> gives me the
>>>>>>
>>>>>> correct
>>>>>>>>
>>>>>>>> rotation of
>>>>>>>>>
>>>>>>>>> the plot. But now it plots x
>> and y
>>> axis (tick
>>>>>>
>>>>>> marks
>>>>>>>>
>>>>>>>> and labels)
>>>>>>>>>
>>>>>>>>> along the top of the plot.
>> Is
>>> there one way to
>>>>>>
>>>>>> plot x
>>>>>>>>
>>>>>>>> and y axis on
>>>>>>>>>
>>>>>>>>> the bottom of the plot?
>>>>>>>>
>>>>>>>> Look at the scpos argument to
>> specify
>>> the scales
>>>>>>
>>>>>> location.
>>>>>>>>
>>>>>>>> (Still
>>>>>>>> lacking an example and
>> therrefore
>>> doing this from
>>>>>>
>>>>>> memory.)
>>>>>>>>
>>>>>>>> --
>>>>>>>> David
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> John
>>>>>>>>>
>>>>>>>>> --- On Wed, 4/7/10, David
>>> Winsemius <dwinsemius at comcast.net>
>>>>>>>>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> From: David Winsemius
>> <dwinsemius at comcast.net>
>>>>>>>>>> Subject: Re: [R] 3-D
>> response
>>> surface
>>>>>>
>>>>>> using
>>>>>>>>
>>>>>>>> wireframe()
>>>>>>>>>>
>>>>>>>>>> To: "array chip" <arrayprofile at yahoo.com>
>>>>>>>>>> Cc: r-help at r-project.org
>>>>>>>>>> Date: Wednesday, April
>> 7,
>>> 2010, 8:07 AM
>>>>>>>>>> A search with the
>> following
>>>>>>>>>> strategy:
>>>>>>>>>>
>>>>>>>>>> RSiteSearch("lattice
>> wireframe
>>> rotate
>>>>>>
>>>>>> axes")
>>>>>>>>>>
>>>>>>>>>> Followed by adding
>> requests to
>>> search
>>>>>>
>>>>>> earlier
>>>>>>>>
>>>>>>>> years'
>>>>>>>>>>
>>>>>>>>>> archives produced this
>> link
>>> which has a
>>>>>>
>>>>>> further
>>>>>>>>
>>>>>>>> link to a
>>>>>>>>>>
>>>>>>>>>> document that answers
>> most of
>>> your
>>>>>>
>>>>>> questions, at
>>>>>>>>
>>>>>>>> least the
>>>>>>>>>>
>>>>>>>>>> ones that are
>> comprehensible:
>>>>>>>>>>
>>>>>>>>>> http://tolstoy.newcastle.edu.au/R/e2/help/07/03/12534.html
>>>>>>>>>>
>>>>>>>>>> --David.
>>>>>>>>>>
>>>>>>>>>> On Apr 6, 2010, at 7:12
>> PM,
>>> array chip
>>>>>>
>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> I am working on
>> plotting a
>>> response
>>>>>>
>>>>>> surface
>>>>>>>>
>>>>>>>> using
>>>>>>>>>>
>>>>>>>>>> wireframe(). The default
>>> style/orientation
>>>>>>
>>>>>> is
>>>>>>>>>>>
>>>>>>>>>>> z
>>>>>>>>>>> |
>>>>>>>>>>> |
>>>>>>>>>>> y |
>>>>>>>>>>> \ |
>>>>>>>>>>> \ |
>>>>>>>>>>> \
>>>>>>
>>>>>> |
>>>>>>>>>>>
>>>>>>>>>>> \
>>>>>>
>>>>>> |
>>>>>>>>>>>
>>>>>> \ |
>>>>>>>>>>>
>>>>>>>>>>> \
>>>>>>
>>>>>> |
>>>>>>>>>>>
>>>>>>>>>>> \ |
>>>>>>>>>>>
>>>>>>>> \|________________x
>>>>>>>>>>>
>>>>>>>>>>> 0
>>>>>>>>>>>
>>>>>>>>>>> Now what I want the
>>> orientation of
>>>>>>
>>>>>> axes is:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> z
>>>>>>>>>>>
>>>>>>>>>> |
>>>>>>>>>>>
>>>>>>>>>> |
>>>>>>>>>>>
>>>>>>>>>> |
>>>>>>>>>>>
>>>>>>>>>> |
>>>>>>>>>>>
>>>>>>>>>> |
>>>>>>>>>>>
>>>>>>>>>> /0\
>>>>>>>>>>>
>>>>>>>>>> / \
>>>>>>>>>>>
>>>>>>>>>> /
>>>>>>
>>>>>> \
>>>>>>>>>>>
>>>>>>>>>> / \
>>>>>>>>>>>
>>>>>>>>>> /
>>>>>>>>
>>>>>>>> \
>>>>>>>>>>>
>>>>>>>> /
>>>>>>>>>>
>>>>>> \
>>>>>>>>>>>
>>>>>> y
>>>>>>>>>>
>>>>>> z
>>>>>>>>>>
>>>>>>>>>> Two z axes? How
>> interesting!
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> My understanding is
>> that
>>> the
>>>>>>>>
>>>>>>>> screen=list(z=,y=,x=)
>>>>>>>>>>
>>>>>>>>>> control the orientation
>> of
>>> axes, but even
>>>>>>
>>>>>> after
>>>>>>>>
>>>>>>>> reading the
>>>>>>>>>>
>>>>>>>>>> help page of screen
>> argument,
>>> I still
>>>>>>
>>>>>> don't
>>>>>>>>
>>>>>>>> understand how
>>>>>>>>>>
>>>>>>>>>> to use it.
>>>>>>>>>>>
>>>>>>>>>>> screen: "A list
>>> determining the
>>>>>>
>>>>>> sequence of
>>>>>>>>
>>>>>>>> rotations
>>>>>>>>>>
>>>>>>>>>> to be applied to the
>> data
>>> before being
>>>>>>
>>>>>> plotted.
>>>>>>>>
>>>>>>>> The initial
>>>>>>>>>>
>>>>>>>>>> position starts with the
>>> viewing point
>>>>>>
>>>>>> along the
>>>>>>>>
>>>>>>>> positive
>>>>>>>>>>
>>>>>>>>>> z-axis, and the x and y
>> axes
>>> in the usual
>>>>>>>>
>>>>>>>> position. Each
>>>>>>>>>>
>>>>>>>>>> component of the list
>> should
>>> be named one
>>>>>>
>>>>>> of "x",
>>>>>>>>
>>>>>>>> "y" or "z"
>>>>>>>>>>
>>>>>>>>>> (repititions are
>> allowed),
>>> with their
>>>>>>
>>>>>> values
>>>>>>>>
>>>>>>>> indicating the
>>>>>>>>>>
>>>>>>>>>> amount of rotation about
>> that
>>> axis in
>>>>>>
>>>>>> degrees."
>>>>>>>>>>>
>>>>>>>>>>> Can anyone explain to
>> me
>>> how the
>>>>>>
>>>>>> screen
>>>>>>>>
>>>>>>>> argument
>>>>>>>>>>
>>>>>>>>>> works? And what values
>> (x,y,z)
>>> I should
>>>>>>
>>>>>> choose for
>>>>>>>>
>>>>>>>> the
>>>>>>>>>>
>>>>>>>>>> orientation that I want?
>>>>>>>>>>>
>>>>>>>>>>> Another question is
>>> wireframe(0 will
>>>>>>
>>>>>> draw all
>>>>>>>>
>>>>>>>> 8 edges
>>>>>>>>>>
>>>>>>>>>> of the cubic by default,
>> is
>>> there anyway
>>>>>>
>>>>>> that I
>>>>>>>>
>>>>>>>> can control
>>>>>>>>>>
>>>>>>>>>> what edges I can draw,
>> what I
>>> can hide?
>>>>>>>>>>>
>>>>>>>>>>> thanks very much!
>>>>>>>>>>>
>>>>>>>>>>> John
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>
>>> ______________________________________________
>>>>>>>>>>>
>>>>>>>>>>> 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.
>>>>>>>>>>
>>>>>>>>>> David Winsemius, MD
>>>>>>>>>> West Hartford, CT
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> David Winsemius, MD
>>>>>>>> West Hartford, CT
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> David Winsemius, MD
>>>>>> West Hartford, CT
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> David Winsemius, MD
>>>> West Hartford, CT
>>>>
>>>> ______________________________________________
>>>> 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.
>>>>
>>>
>>>
>>>
>>> --
>>> Felix Andrews / 安福立
>>> Postdoctoral Fellow
>>> Integrated Catchment Assessment and Management (iCAM)
>>> Centre
>>> Fenner School of Environment and Society [Bldg 48a]
>>> The Australian National University
>>> Canberra ACT 0200 Australia
>>> M: +61 410 400 963
>>> T: + 61 2 6125 4670
>>> E: felix.andrews at anu.edu.au
>>> CRICOS Provider No. 00120C
>>> --
>>> http://www.neurofractal.org/felix/
>>>
>>
>>
>>
>> -----Inline Attachment Follows-----
>>
>> ______________________________________________
>> 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.
>>
>
>
> ______________________________________________
> 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.
David Winsemius, MD
West Hartford, CT
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