[R] Smoothed 3D plots

From: Jorge Ivan Velez <jorgeivanvelez_at_gmail.com>
Date: Wed, 26 Nov 2008 13:41:18 -0500


DeaR list,

I'm trying to represent some information via 3D plots. My data and session info are at the end of this message. So far, I have tried scatterplot3d (scatterplot3d),
persp3d (rgl), persp (graphics) and scatter3d (Rmcdr) but any of them gave me what I'd like to have as final result (please see [1] for a similar 3D plot changing
PF by ypred, pdn by h4 and pup by h11).

In general terms, I would like to plot a smoothed surface with h4 and h11 in the x and y axis, respectively, and y in the z axis. I think that a smoothing procedure should
work but I don't know how to get that work in R.

I would really appreciate any help you can provide me.

Thanks in advance,

Jorge Velez

[1] http://www.meyersanalytics.com/pfpuppdn.gif

# -------
# Data
# -------

res=structure(list(ypred = c(0.718230085350727, 0.654361814214854,
0.644756374003864, 0.652006785905442, 0.695903817103918, 0.812977870063322,
0.639339808892218, 0.701034703527025, 0.740110233651808, 0.664942946000872,
0.866847509624424, 0.652502006511821, 0.650617983864292, 0.713152860580267,
0.717738908917513, 0.738697216666161, 0.666120460155577, 0.652242288736383,
0.596880009623886, 0.671197684926038, 0.45, 0.820174620312253,
0.665066954282449, 0.735164674202043, 0.696027875479989, 0.646119215131913,
0.644235192484384, 0.663550099786557), h4 = c(1, 0, 1, 0, 1,
1, 1, 0, 0, 0, 1, 2, 2, 1, 0, 0, 0, 0, 2, 0, 2, 1, 1, 0, 0, 0,
0, 1), h11 = c(0, 0, 1, 0, 1, 2, 1, 0, 1, 2, 2, 1, 1, 0, 2, 1,
2, 0, 1, 2, 2, 2, 0, 1, 1, 0, 0, 0)), .Names = c("y", "h4", "h11"), class = "data.frame", row.names = c(NA, -28L))
# ------------
# Some plots
# ------------

# Option 1
require(Rcmdr)
with(res,
scatter3d(h4,ypred,h11, xlab='Chr4',zlab='Chr11', ylab='Ratio',fit=c("linear","quadratic")) )

# Option 2
require(scatterplot3d)
with(res,
scatterplot3d(h4,ypred,h11, xlab='Chr4',zlab='Chr11',ylab='Ratio') )

# -------------
# Session info
# -------------

R version 2.8.0 Patched (2008-11-08 r46864) i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods
base

other attached packages:
[1] rgl_0.81 mgcv_1.4-1 Rcmdr_1.4-4 car_1.2-9

[5] scatterplot3d_0.3-27 lattice_0.17-15

loaded via a namespace (and not attached):
[1] grid_2.8.0

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