[R] 3-D response surface using wireframe()
array chip
arrayprofile at yahoo.com
Fri Apr 9 21:27:15 CEST 2010
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.
>
More information about the R-help
mailing list