Re: [R] MDS in 3D

From: Atte Tenkanen <attenka_at_utu.fi>
Date: Sun 07 Jan 2007 - 23:03:36 GMT

> 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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