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 <fe...@nfrac.org> wrote:
> From: Felix Andrews <fe...@nfrac.org>
> Subject: Re: [R] 3-D response surface using wireframe()
> To: "David Winsemius" <dwinsem...@comcast.net>
> Cc: "array chip" <arrayprof...@yahoo.com>, r-help@r-project.org
> Date: Thursday, April 8, 2010, 9:56 PM
> On 9 April 2010 11:18, David
> Winsemius <dwinsem...@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 <dwinsem...@comcast.net>
> wrote:
> >>
> >>> From: David Winsemius <dwinsem...@comcast.net>
> >>> Subject: Re: [R] 3-D response surface using
> wireframe()
> >>> To: "array chip" <arrayprof...@yahoo.com>
> >>> Cc: r-help@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 <dwinsem...@comcast.net>
> >>>
> >>> wrote:
> >>>>
> >>>>> From: David Winsemius <dwinsem...@comcast.net>
> >>>>> Subject: Re: [R] 3-D response surface
> using
> >>>
> >>> wireframe()
> >>>>>
> >>>>> To: "array chip" <arrayprof...@yahoo.com>
> >>>>> Cc: r-help@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 <dwinsem...@comcast.net>
> >>>>>
> >>>>> wrote:
> >>>>>>
> >>>>>>> From: David Winsemius <dwinsem...@comcast.net>
> >>>>>>> Subject: Re: [R] 3-D response
> surface
> >>>
> >>> using
> >>>>>
> >>>>> wireframe()
> >>>>>>>
> >>>>>>> To: "array chip" <arrayprof...@yahoo.com>
> >>>>>>> Cc: r-help@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@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@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.andr...@anu.edu.au
> CRICOS Provider No. 00120C
> --
> http://www.neurofractal.org/felix/
>
x y z
1 0 0 1.40496188674186
2 0.25 0 0.800015588666326
3 0.5 0 0.195069290590796
4 0.75 0 -0.409877007484734
5 1 0 -1.01482330556026
6 1.25 0 -1.61976960363579
7 1.5 0 -2.22471590171132
8 1.75 0 -2.82966219978686
9 2 0 -3.43460849786239
10 2.25 0 -4.03955479593792
11 2.5 0 -4.64450109401345
12 0 2.5 1.00257090162757
13 0.25 2.5 0.369516016300772
14 0.5 2.5 -0.263538869026027
15 0.75 2.5 -0.896593754352826
16 1 2.5 -1.52964863967962
17 1.25 2.5 -2.16270352500642
18 1.5 2.5 -2.79575841033322
19 1.75 2.5 -3.42881329566002
20 2 2.5 -4.06186818098682
21 2.25 2.5 -4.69492306631362
22 2.5 2.5 -5.32797795164042
23 0 5 0.600179916513286
24 0.25 5 -0.0609835560647821
25 0.5 5 -0.72214702864285
26 0.75 5 -1.38331050122092
27 1 5 -2.04447397379898
28 1.25 5 -2.70563744637705
29 1.5 5 -3.36680091895512
30 1.75 5 -4.02796439153319
31 2 5 -4.68912786411126
32 2.25 5 -5.35029133668932
33 2.5 5 -6.01145480926739
34 0 7.5 0.197788931399
35 0.25 7.5 -0.491483128430336
36 0.5 7.5 -1.18075518825967
37 0.75 7.5 -1.87002724808901
38 1 7.5 -2.55929930791835
39 1.25 7.5 -3.24857136774768
40 1.5 7.5 -3.93784342757702
41 1.75 7.5 -4.62711548740635
42 2 7.5 -5.31638754723569
43 2.25 7.5 -6.00565960706503
44 2.5 7.5 -6.69493166689436
45 0 10 -0.204602053715285
46 0.25 10 -0.92198270079589
47 0.5 10 -1.63936334787650
48 0.75 10 -2.3567439949571
49 1 10 -3.07412464203771
50 1.25 10 -3.79150528911831
51 1.5 10 -4.50888593619892
52 1.75 10 -5.22626658327952
53 2 10 -5.94364723036013
54 2.25 10 -6.66102787744073
55 2.5 10 -7.37840852452134
56 0 12.5 -0.606993038829571
57 0.25 12.5 -1.35248227316144
58 0.5 12.5 -2.09797150749332
59 0.75 12.5 -2.84346074182519
60 1 12.5 -3.58894997615707
61 1.25 12.5 -4.33443921048894
62 1.5 12.5 -5.07992844482081
63 1.75 12.5 -5.82541767915269
64 2 12.5 -6.57090691348456
65 2.25 12.5 -7.31639614781643
66 2.5 12.5 -8.06188538214831
67 0 15 -1.00938402394386
68 0.25 15 -1.782981845527
69 0.5 15 -2.55657966711014
70 0.75 15 -3.33017748869328
71 1 15 -4.10377531027643
72 1.25 15 -4.87737313185957
73 1.5 15 -5.65097095344271
74 1.75 15 -6.42456877502585
75 2 15 -7.198166596609
76 2.25 15 -7.97176441819214
77 2.5 15 -8.74536223977528
78 0 17.5 -1.41177500905814
79 0.25 17.5 -2.21348141789255
80 0.5 17.5 -3.01518782672696
81 0.75 17.5 -3.81689423556137
82 1 17.5 -4.61860064439579
83 1.25 17.5 -5.4203070532302
84 1.5 17.5 -6.22201346206461
85 1.75 17.5 -7.02371987089902
86 2 17.5 -7.82542627973343
87 2.25 17.5 -8.62713268856784
88 2.5 17.5 -9.42883909740225
89 0 20 -1.81416599417243
90 0.25 20 -2.64398099025811
91 0.5 20 -3.47379598634379
92 0.75 20 -4.30361098242947
93 1 20 -5.13342597851515
94 1.25 20 -5.96324097460083
95 1.5 20 -6.79305597068651
96 1.75 20 -7.62287096677219
97 2 20 -8.45268596285787
98 2.25 20 -9.28250095894355
99 2.5 20 -10.1123159550292
100 0 22.5 -2.21655697928671
101 0.25 22.5 -3.07448056262366
102 0.5 22.5 -3.93240414596061
103 0.75 22.5 -4.79032772929756
104 1 22.5 -5.64825131263451
105 1.25 22.5 -6.50617489597145
106 1.5 22.5 -7.3640984793084
107 1.75 22.5 -8.22202206264535
108 2 22.5 -9.0799456459823
109 2.25 22.5 -9.93786922931925
110 2.5 22.5 -10.7957928126562
111 0 25 -2.618947964401
112 0.25 25 -3.50498013498922
113 0.5 25 -4.39101230557743
114 0.75 25 -5.27704447616565
115 1 25 -6.16307664675387
116 1.25 25 -7.04910881734208
117 1.5 25 -7.9351409879303
118 1.75 25 -8.82117315851852
119 2 25 -9.70720532910674
120 2.25 25 -10.5932374996950
121 2.5 25 -11.4792696702832
______________________________________________
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.
