Re: [R] MDS in 3D

From: Atte Tenkanen <attenka_at_utu.fi>
Date: Sun 07 Jan 2007 - 23:04:47 GMT

...and my system is OSX 10.4.

Atte

>
> > Hi,
> >
> > I have tried to develop multidimensional scaling for 3D space
> using

> > PCA without success, yet;-) Is there some application ready in R?
> >
> > Cheers,
> >
> > Atte
> >
>
> I found xgobi, but when I try to run example I get some command not

> found -errors.
>
> Atte
>
>
> > data(morsecodes) ## from the XGobi/XGvis data, see ?morsecodes
> > mc.row <- paste(morsecodes.row[,1],morsecodes.row[,2])
> >
> > xgvis(dmat = morsecodes.dist,
> + pos = morsecodes.pos,
> + rowlab = mc.row,
> + colors = morsecodes.colors,
> + glyphs = morsecodes.glyphs,
> + lines = morsecodes.lines,
> + linecolors = morsecodes.linecolors)
> xgvis /tmp/RtmpDaR3cT/xgvis-6058ed8 &
> >
> > ##> 2) Show lines by hitting "l" with the mouse over the plot.
> > ##> 3) Examine morsecode labels by hitting "i" and mousing
> around on the plot.
> > ##> 3b) Press "r" (on the plot) to switch 3D rotation in xgobi.
> > ##> 4) Run MDS in 3D by clicking "Run MDS" (in xgvis).
> > ##> 5) Speed up the optimization by increasing the "Stepsize"
> with the slider.
> > ##> The "Stress function" value may go as low as 0.1925 (MM).
> > ##> 6) When the optimization calms down, click "Run MDS" to
> toggle MDS off.
> > ##> 7) Rotate the MDS configuration in 3D {by "r" with mouse
> over plot}.
> > ##> 8) Increase the rotation speed with the slider in the top
> left and
> > ##> control the rotation direction by dragging the mouse on
> the plot.
> > ##> 9) You can check out the initial configuration by
> >
> > ## In order to have no color warning :
> > Mcolors <- unique(morsecodes.colors)
> /bin/sh: line 1: xgvis: command not found
> > (Mcolors <- paste("*brushColor", 0:(length(Mcolors)-1),": ",
> Mcolors, sep=""))
> [1] "*brushColor0: SkyBlue" "*brushColor1: Green"
> [3] "*brushColor2: Yellow" "*brushColor3: HotPink"
> [5] "*brushColor4: Red"
> >
> > xgobi(morsecodes.pos, collab = morsecodes.col, rowlab = mc.row,
> + colors = morsecodes.colors,
> + glyphs = morsecodes.glyphs,
> + lines = morsecodes.lines,
> + linecolors = morsecodes.linecolors,
> + resources= c("*showLines: True", Mcolors))
> xgobi -title 'morsecodes.pos' -std mmx /tmp/RtmpDaR3cT/xgobi-
> mrscd56e509fe &
> /bin/sh: line 1: xgobi: command not found
> >
> > ##> This XGobi window will be linked with
> > ##> the XGvis window for glyph-color brushing and labeling.
>



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