[R] scatter3D and colours

[Jorge I Velez]

Dear R-help,

I am using the plot3D package to produce 3D spheres along with 95% CIs
distinguishing each sphere with a predefined colour (see the reproducible
example at the end).

I have been successful in producing a similar plot using a different data
set (kindly see
https://www.dropbox.com/s/snpgiqgqaiqgpiv/exp1combined.pdf?dl=0), but in
this case I cannot arrange the colours as desired. Specifically, the
colours obtaind do not correspond to those in the "cols" object below (kindly
see https://www.dropbox.com/s/nhljsuare84g811/test_exp2.pdf?dl=0).

Any help/tips would be greatly appreciated.

Thank you very much in advance.

Best regards,
Jorge Velez.-


## package needed
if(!require(plot3D)) install.packages("plot3D")
require(plot3D)

## data to be plotted
d0 <- structure(list(X = c(2.5, -2, 1), Z = c(-3.5, 4, -1), Y = c(8,
-8.5, -1)), .Names = c("X", "Z", "Y"), row.names = c("high",
"low", "medium"), class = "data.frame")
d0

## confidence intervals to be added
CI2 <- structure(list(z = structure(c(2, 3, 4, 2, 3, 4), .Dim = c(3L,
2L), .Dimnames = list(c("high", "low", "medium"), c("97.5%",
"97.5%"))), y = structure(c(4, 5, 5, 4, 5, 5), .Dim = c(3L, 2L
), .Dimnames = list(c("high", "low", "medium"), c("97.5%", "97.5%"
))), x = structure(c(3, 7, 5, 3, 7, 5), .Dim = c(3L, 2L), .Dimnames = list(
    c("high", "low", "medium"), c("97.5%", "97.5%"))), alen = 0,
    lwd = 2), .Names = c("z", "y", "x", "alen", "lwd"))

## colours I would like to have
cols <- c("#0080ff", "#ff00ff", "darkgreen")

# this produces the 3D plot, but the colours are not properly assigned
with(d0, scatter3D(X, Z, Y, bty = "b2", col = cols,
           pch = 20, cex = 4, ticktype = "detailed", colkey = FALSE, phi =
20, theta = -140, zlim = c(-14, 14), xlim = c(-14, 14), ylim = c(-14, 14),
xlab = "X", ylab = "Z", zlab = "Y", CI = CI2))
mtext('Experiment 2', line = -0.5, side = 3, cex = 1.3)


​## R session details
R> sessionInfo()
R version 3.2.4 Patched (2016-03-28 r70416)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  parallel  compiler
[8] methods   base

other attached packages:
[1] plot3D_1.1   readxl_0.1.1

loaded via a namespace (and not attached):
[1] tools_3.2.4  misc3d_0.8-4 Rcpp_0.12.5

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