David, Eduardo,
Thanks for the code. I have run it and I'm not sure what to do with the
graph when it comes up. Can I interact with it, such as an RGL graph? I've
tried clicking or dragging with the mouse and nothing happens. My system is
a Windows Vista and R2.9.
Best,
Iuri.
On Mon, Nov 2, 2009 at 7:35 PM, David Winsemius <dwinsem...@comcast.net>wrote:
> The attached file did not come through to the list. I think you have some
> non-standard characters (or at least non-standard in my locale). I was able
> to get the code to run after using the Zap Gremlins function in
> TextWrangler. Prior to that "treatment" pretty much every line threw an
> error of this sort:
>
>
> > setClass(Class = 'POI',
> + representation(matrizSim = 'matrix',cos.query.docs = 'vector',
> Error: unexpected input in:
> "setClass(Class = 'POI',
> ¬"
>
> > wordsInQuery = 'ANY',docs = 'matrix', objeto = 'matrix', objetoC
> Error: unexpected input in "¬"
> > = 'matrix',
> Error: unexpected '=' in "="
>
> > Pcoords = 'matrix', PcoordsFI = 'matrix', newPcoords = 'matrix',
> Error: unexpected input in "¬"
> > newcoords = 'numeric' ,
> Error: unexpected ',' in "newcoords = 'numeric' ,"
>
> > newcoords_1 = 'numeric', M = 'numeric', poisTextCol =
> Error: unexpected input in "¬"
>
> I also needed to remove a couple of spaces between function names and
> parentheses when these occurred at ends-of-lines. Attached is a working
> version as a .txt file (which should make it through the list-serv:
>
>
>
>
>
> -- David.
> > sessionInfo()
> R version 2.10.0 Patched (2009-10-29 r50258)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] rms_2.1-0 Hmisc_3.7-0 survival_2.35-7
>
> loaded via a namespace (and not attached):
> [1] cluster_1.12.1 grid_2.10.0 lattice_0.17-26
>
>
>
>
> On Nov 2, 2009, at 3:43 PM, eduardo san miguel wrote:
>
> I send r-code in an attached file.
>>
>> 2009/11/2 Iuri Gavronski <i...@proxima.adm.br>:
>>
>>> Eduardo,
>>>
>>> Would you mind sending me the R code in an attached file. Your code
>>> didn't
>>> work here and I am not sure it is because of line breaks from the email
>>> program.
>>>
>>> Iuri.
>>>
>>> On Mon, Nov 2, 2009 at 10:53 AM, eduardo san miguel <
>>>
>> eduardosa...@gmail.com>
>>
>>> wrote:
>>>
>>>>
>>>> Hello all,
>>>>
>>>> I have almost finished the development of a new package where ideas
>>>> from Tamara Munzner, George Furnas and Costa and Venturini are
>>>> implemented.
>>>>
>>>> 1.- Da Costa, David & Venturini, Gilles (2006). An Interactive
>>>> Visualization Environment for Data Exploration Using Points of
>>>> Interest. adma 2006: 416-423
>>>>
>>>> 2.- Furnas, George (1986). Generalized Fisheye Views. Human Factors in
>>>> computing systems, CHI '86 conference proceedings, ACM, New York, pp.
>>>> 16-23.
>>>>
>>>> 3.- Heidi Lam, Ronald A. Rensink, and Tamara Munzner (2006). Effects
>>>> of 2D Geometric Transformations on Visual Memory. Proc. Applied
>>>> Perception in Graphics and Visualization (APGV 2006), 119-126, 2006.
>>>>
>>>> 4.- Keith Lau, Ron Rensink, and Tamara Munzner (2004). Perceptual
>>>> Invariance of Nonlinear Focus+Context Transformations. Proc. First
>>>> Symposium on Applied Perception in Graphics and Visualization (APGV
>>>> 04) 2004, pp 65-72.
>>>>
>>>> This is a sample with some basic functionality and a VERY BASIC
>>>> example with kmeans plotting.
>>>>
>>>> Comments will be greatly appreciated.
>>>>
>>>> Regards
>>>>
>>>> -- R CODE
>>>> require(methods)
>>>>
>>>> setClass(Class = 'POI',
>>>> representation(matrizSim = 'matrix',cos.query.docs = 'vector',
>>>> wordsInQuery = 'ANY',docs = 'matrix', objeto = 'matrix', objetoC
>>>> = 'matrix',
>>>> Pcoords = 'matrix', PcoordsFI = 'matrix', newPcoords = 'matrix',
>>>> newcoords = 'numeric' ,
>>>> newcoords_1 = 'numeric', M = 'numeric', poisTextCol =
>>>> 'character' , colores = 'vector' ,
>>>> poisCircleCol = 'character' , linesCol = 'character', itemsCol =
>>>> 'character',
>>>> LABELS = 'logical', vscale = 'numeric', hscale = 'numeric',
>>>> circleCol = 'character',
>>>> plotCol = 'character', itemsFamily = 'character', lenteDefault
>>>> = 'numeric',
>>>> zoomDefault = 'numeric' , rateDefault = 'numeric' ,
>>>> topKDefault = 'numeric' ,
>>>> pal = 'character', selected = 'numeric' , circRadio =
>>>> 'numeric' , IncVscale = 'numeric',
>>>> cgnsphrFont = 'numeric', xClick_old = 'numeric', yClick_old =
>>>> 'numeric',
>>>> wordsInQueryFull = 'character' ),
>>>> prototype(cos.query.docs = 0, colores = 0, newcoords = 0,
>>>> newcoords_1 = 0, M = 3,
>>>> vscale = 0.5 , hscale = 1.5 , circleCol = 'black' ,
>>>> itemsCol = 'white',
>>>> poisTextCol = '#fff5ee', poisCircleCol = '#fff5ee',
>>>> linesCol = 'white',
>>>> plotCol = 'black', itemsFamily = 'sans', lenteDefault =
>>>> 1, zoomDefault = 15 ,
>>>> rateDefault = 0.1 , topKDefault = 25, pal = 'topo' ,
>>>> selected = 1 ,
>>>> circRadio = 0.25 , IncVscale = 0.05 , cgnsphrFont =
>>>> 1.01, LABELS = T)
>>>> )
>>>>
>>>> setGeneric("puntosMedios" ,
>>>> function(Pcoords, detalle = 5){standardGeneric
>>>> ("puntosMedios")})
>>>>
>>>> setMethod("puntosMedios" ,
>>>> signature = "matrix",
>>>> function(Pcoords, detalle = 5){
>>>>
>>>> for (i in 1:detalle){
>>>> new_pcoords = matrix(rep(0,4*nrow(Pcoords)), nrow = 2*
>>>> nrow(Pcoords), byrow = T )
>>>> cont = 0
>>>> for (i in 1:nrow(Pcoords)){
>>>> if (i == nrow(Pcoords)) {
>>>> cont = cont + 1
>>>> new_pcoords[cont,] = Pcoords[i,]
>>>> cont = cont + 1
>>>> new_pcoords[cont,] = Pcoords[i,] -
>>>> ((Pcoords[i,]-Pcoords[1,])/2)
>>>> }else{
>>>> cont = cont + 1
>>>> new_pcoords[cont,] = Pcoords[i,]
>>>> cont = cont + 1
>>>> new_pcoords[cont,] = Pcoords[i,] -
>>>> ((Pcoords[i,]-Pcoords[i+1,])/2)}}
>>>> Pcoords = new_pcoords}
>>>> return(Pcoords)
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("fishIout" ,
>>>> function(x, value){standardGeneric ("fishIout")})
>>>>
>>>> setMethod("fishIout" ,
>>>> signature = "numeric",
>>>> function(x, value){
>>>>
>>>> d = value
>>>> if (x > 0){
>>>> signo = 1
>>>> }else{
>>>> signo = -1
>>>> }
>>>> x = abs(x)
>>>> return(signo*(-(x/((d*x)-d-1))))
>>>> }
>>>> )
>>>>
>>>> setGeneric("fishIin" ,
>>>> function(x, value){standardGeneric ("fishIin")})
>>>>
>>>> setMethod("fishIin" ,
>>>> signature = "numeric",
>>>> function(x, value){
>>>>
>>>> d = value
>>>> if (x > 0){
>>>> signo = 1
>>>> }else{
>>>> signo = -1
>>>> }
>>>> x = abs(x)
>>>>
>>>> return(signo*(((d+1)*x)/(d*x+1)))
>>>> }
>>>> )
>>>>
>>>> setGeneric("toPolar" ,
>>>> function(x, y){standardGeneric ("toPolar")})
>>>>
>>>> setMethod("toPolar" ,
>>>> signature = "numeric",
>>>> function(x, y){
>>>>
>>>> t1 = atan2(y,x)
>>>> rP = sqrt(x^2+y^2)
>>>> return(c(t1 = t1,rP = rP))
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("toCartesian" ,
>>>> function(t1, rP){standardGeneric ("toCartesian")})
>>>>
>>>> setMethod("toCartesian" ,
>>>> signature = "numeric",
>>>> function(t1, rP){
>>>>
>>>> x1 = rP*cos(t1)
>>>> y1 = rP*sin(t1)
>>>> return(c(x = x1,y = y1))
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("circulo" ,
>>>> function(cx, cy, r, circleCol, PLOT =
>>>> TRUE){standardGeneric ("circulo")})
>>>>
>>>> setMethod("circulo" ,
>>>> signature = "numeric",
>>>> function(cx, cy, r, circleCol, PLOT = TRUE){
>>>>
>>>> t = seq(0,2*pi,length=100)
>>>> circle = t(rbind(cx+sin(t)*r,cy+cos(t)*r))
>>>> if (PLOT == TRUE)
>>>> plot(circle,type='l',,ylim=c(-1.15,1.15),xlim=c(-1.15,1.15),
>>>> ann=FALSE, axes=F, col = circleCol)
>>>> return(circle)
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("circulin" ,
>>>> function(cx, cy, r = 0.045,
>>>> objeto, col = 'blue', PLOT = TRUE, label = 0){
>>>> standardGeneric ("circulin")})
>>>>
>>>> setMethod("circulin" ,
>>>> signature = "ANY",
>>>> function(cx, cy, r = 0.045, objeto, col = 'blue', PLOT =
>>>> TRUE, label = 0){
>>>>
>>>> t = seq(0,2*pi,length=100)
>>>> circle = t(rbind(cx+sin(t)*r,cy+cos(t)*r))
>>>> points(circle,type='l', col = col)
>>>> if (label != 0) text(cx,cy,label,cex = .7)
>>>> insiders <-
>>>> apply(objeto,1,function(co)(cx-co[1])^2+(cy-co[2])^2<r^2)
>>>> assign('insiders', insiders , envir = POI.env)
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("addNoise" ,
>>>> function(m, tamanyo = 0.01){standardGeneric ("addNoise")})
>>>>
>>>> setMethod("addNoise" ,
>>>> signature = "matrix",
>>>> function(m, tamanyo = 0.01){
>>>>
>>>> noise = function(m, t = tamanyo){
>>>> ruido = rnorm(length(m), 0,t)
>>>> return(m+ruido)
>>>> }
>>>> noised = noise(m)
>>>> unicos = which(duplicated(m) == FALSE)
>>>> m[-unicos,] = noised[-unicos,]
>>>> return(m)
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("toHiperbolico" ,
>>>> function(objeto, M = 1 , cx = 0, cy = 0, r = 1){
>>>> standardGeneric ("toHiperbolico")})
>>>>
>>>> setMethod("toHiperbolico" ,
>>>> signature = "matrix",
>>>> function(objeto, M = 1 , cx = 0, cy = 0, r = 1){
>>>>
>>>> insiders =
>>>> apply(objeto,1,function(co)(cx-co[1])^2+(cy-co[2])^2<r^2)
>>>> outers = which(insiders < 1)
>>>> objetoP = matrix(toPolar(objeto[,1],objeto[,2]),nc=2)
>>>> if (length(outers)){
>>>> objetoP[outers,2] = 1
>>>> }
>>>> objetoP[,2] = sapply(objetoP[,2],fishIin,M)
>>>> objetoC = matrix(toCartesian(objetoP[,1],objetoP[,2]),nc=2)
>>>> return(list(objetoC = objetoC,
>>>> objetoP = objetoP))
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("POIcoords<-" , function(object, value){standardGeneric
>>>> ("POIcoords<-")})
>>>>
>>>> setReplaceMethod( f ="POIcoords",
>>>> signature = 'POI',
>>>> definition = function(object, value){
>>>> obj...@pcoords <- value$Pcoords
>>>> obj...@pcoordsfi <- value$PcoordsFI
>>>> obj...@newpcoords <- value$newPcoords
>>>> obj...@objeto <- value$objeto
>>>>
>>>> return(object)
>>>> }
>>>> )
>>>>
>>>> setGeneric("POICalc" ,
>>>> function(objeto, NC, cx=0, cy=0, r=1,
>>>> ...){standardGeneric ("POICalc")})
>>>>
>>>> setMethod("POICalc" ,
>>>> signature = "POI",
>>>> function(objeto, NC, cx=0, cy=0, r=1, ...){
>>>>
>>>> MatrizSim = obj...@matrizsim
>>>> secuencia = seq(2/NC,2,2/NC)
>>>> Pcoords = matrix(rep(0,NC*2),nc=2)
>>>> n = 1
>>>> for (i in secuencia){
>>>> Pcoords[n,] = c(r * cos(i*pi), r * sin(i*pi))
>>>> n = n+1
>>>> }
>>>> PcoordsFI = matrix(toPolar(Pcoords[,1],Pcoords[,2]),nc=2)
>>>> PcoordsFI[,2] = PcoordsFI[,2]+.15
>>>> PcoordsFI = matrix(toCartesian(PcoordsFI[,1],PcoordsFI[,2]),nc=2)
>>>>
>>>> if (nrow(Pcoords) != 1){
>>>> newPcoords = puntosMedios(Pcoords)
>>>> } else {
>>>> newPcoords = Pcoords
>>>> }
>>>>
>>>> MatrizSim[is.nan(MatrizSim/rowSums(MatrizSim))] <- 0
>>>>
>>>> W = MatrizSim / rowSums(MatrizSim)
>>>> W[is.nan(W)] <- 0
>>>> nwords = nrow(W)
>>>> objeto = matrix(rep(0,2*nwords),nc=2)
>>>> for (j in 1:nwords){
>>>> for (nPOI in 1:NC){
>>>> objeto[j,1] = objeto[j,1]+(W[j,nPOI]*Pcoords[nPOI,1])
>>>> objeto[j,2] = objeto[j,2]+(W[j,nPOI]*Pcoords[nPOI,2])
>>>> }
>>>> }
>>>>
>>>> objeto = addNoise(objeto)
>>>>
>>>> return(list(Pcoords = Pcoords,
>>>> PcoordsFI = PcoordsFI,
>>>> newPcoords = newPcoords,
>>>> objeto = objeto))
>>>>
>>>> }
>>>> )
>>>>
>>>> setGeneric("POIPlot" ,
>>>> function(POI){standardGeneric ("POIPlot")})
>>>>
>>>> setMethod("POIPlot" ,
>>>> signature = "POI",
>>>> function(POI){
>>>>
>>>> par(bg=...@plotcol, mar = c(0.1,0.1,0.1,0.1), family = p...@itemsfamily
>>>> )
>>>>
>>>>
>>>> if (exists('POI.env')) {
>>>> if (exists('POI', envir = POI.env)) {
>>>> POI <- get('POI', envir = POI.env)
>>>> }
>>>> }
>>>>
>>>> selected = p...@selected
>>>> objeto = p...@objeto
>>>> newcoords = p...@newcoords
>>>> newcoords_1 = p...@newcoords_1
>>>> NC = length(p...@wordsinquery)
>>>> cx=0
>>>> cy=0
>>>> r=1
>>>> etiq2 = p...@docs[,1]
>>>> etiq = p...@wordsinquery
>>>> fishEYE = TRUE
>>>> M = p...@m
>>>> poisTextCol = p...@poistextcol
>>>> colores = p...@colores[poi@docs]
>>>> poisCircleCol = p...@poiscirclecol
>>>> linesCol = p...@linescol
>>>> itemsCol = p...@itemscol
>>>> circleCol = p...@circlecol
>>>> LABELS = p...@labels
>>>> Pcoords = p...@pcoords
>>>> newPcoords = p...@newpcoords
>>>> cgnsphrFont = p...@cgnsphrfont
>>>>
>>>> newcoords_par = newcoords
>>>>
>>>> newcoords_Pcoords = matrix(rep( c(newcoords,newcoords_1 ),
>>>> nrow(Pcoords)),nc=2,byrow=TRUE)
>>>>
>>>> newcoords_puntosMediosPcoords = matrix(rep( c(newcoords,newcoords_1),
>>>>
>>>> nrow(newPcoords)),nc=2,byrow=TRUE)
>>>>
>>>> newcoords = matrix(rep( c(newcoords,newcoords_1),
>>>> nrow(objeto)),nc=2,byrow=TRUE)
>>>>
>>>> objeto = objeto+newcoords
>>>> objetoH = toHiperbolico(objeto, M)
>>>> objetoC = objetoH$objetoC
>>>> objetoP = objetoH$objetoP
>>>>
>>>> Pcoords = Pcoords + newcoords_Pcoords
>>>> PcoordsH = toHiperbolico(Pcoords, M)
>>>> PcoordsC = PcoordsH$objetoC
>>>> PcoordsP = PcoordsH$objetoP
>>>>
>>>> newPcoords = newPcoords + newcoords_puntosMediosPcoords
>>>> newPcoordsH = toHiperbolico(newPcoords, M)
>>>> Pcoords_objetoC = newPcoordsH$objetoC
>>>>
>>>> if (LABELS) {
>>>> PcoordsFI = matrix(toPolar(PcoordsC[,1],PcoordsC[,2]),nc=2)
>>>> PcoordsFI[,2] = 1 +.15
>>>> PcoordsFI = matrix(toCartesian(PcoordsFI[,1],PcoordsFI[,2]),nc=2)
>>>> }
>>>>
>>>> plot(circulo(0,0,1, circleCol, PLOT =
>>>> FALSE),cex=.5,ylim=c(-1.15,1.15),xlim=c(-1.15,1.15),
>>>> ann=FALSE, axes=F,type='l', col = circleCol)
>>>>
>>>> points(objetoC, pch=19, col = colores, cex = 1.5 - objetoP[,2])
>>>>
>>>> text(objetoC[,1], objetoC[,2], labels = etiq2, cex = cgnsphrFont -
>>>> objetoP[,2],
>>>> pos = 3, col = itemsCol)
>>>>
>>>> abline(h = cx, col = 'grey', lty = 'dashed')
>>>> abline(v = cy, col = 'grey', lty = 'dashed')
>>>>
>>>>
>>>> points(PcoordsC,cex = 2, col = poisCircleCol)
>>>>
>>>> lines(Pcoords_objetoC, col = linesCol)
>>>>
>>>>
>>>>
>>>> segments(Pcoords_objetoC[nrow(Pcoords_objetoC),1],Pcoords_objetoC[nrow(Pcoords_objetoC),2],
>>
>>> Pcoords_objetoC[1,1],Pcoords_objetoC[1,2], col = linesCol)
>>>>
>>>> if (LABELS) {
>>>> text(PcoordsFI[,1],PcoordsFI[,2],toupper(etiq),cex=.75, col =
>>>> poisTextCol)
>>>> }
>>>>
>>>> if (selected != 1) {
>>>> circulin(0,0, .5, objeto = objetoC) # probando
>>>> }
>>>>
>>>> if (!exists('POI.env')){
>>>> POI.env <<- new.env()
>>>> }
>>>> poiCOPY = POI
>>>> poic...@objeto <- objeto
>>>> poic...@objetoc <- objetoC
>>>> poic...@newpcoords <- newPcoords
>>>> poic...@pcoords <- Pcoords
>>>> assign('POI',poiCOPY , envir = POI.env)
>>>>
>>>> }
>>>> )
>>>>
>>>>
>>>> # *strong*VERY*strong* basic kmeans example with 6 clusters and 10
>>>> variables
>>>> x <- matrix(rnorm(100, mean = 1, sd = .3), ncol = 10)
>>>> x <- rbind(x,matrix(rnorm(200, mean = 5, sd = .3), ncol = 10))
>>>> x <- rbind(x,matrix(rnorm(100, mean = 10, sd = .3), ncol = 10))
>>>> x <- rbind(x,matrix(rnorm(100, mean = 15, sd = .3), ncol = 10))
>>>> x <- rbind(x,matrix(rnorm(200, mean = 20, sd = .3), ncol = 10))
>>>> x <- rbind(x,matrix(rnorm(100, mean = 25, sd = .3), ncol = 10))
>>>>
>>>> cl <- kmeans(x, 6, iter.max = 100 ,nstart = 25)
>>>>
>>>> # *strong*VERY*strong* basic way of reordering cluster output for
>>>> better plotting
>>>> # here we reorder using just the first cluster
>>>> reorder.cl <- as.numeric(names(sort(rank((as.matrix(dist(cl$centers,
>>>> diag = T)))[,1]))))
>>>> cl$centers <- cl$centers[reorder.cl, ]
>>>> cl$size <- cl$size[reorder.cl]
>>>>
>>>> # distance matrix between each element and its cluster center
>>>> matrizSim = matrix(rep(0, nrow(cl$centers) * nrow(x)), ncol =
>>>> nrow(cl$centers))
>>>> for (n in 1:nrow(cl$centers)){
>>>> for (i in 1:nrow(x)) {
>>>> a = x[i,]
>>>> b = cl$centers[n,]
>>>> matrizSim[[i,n]] = dist(rbind(a,b)) # eucl dist
>>>> }
>>>> }
>>>>
>>>> # From dist to similarity (0 - 1)
>>>> matrizSim = 1 - (matrizSim / rowSums(matrizSim) )
>>>> # exagerate similarity
>>>> matrizSim = matrizSim^3
>>>>
>>>> # Create POI plot
>>>> clusterPOI = new('POI')
>>>> cluster...@m = 1 # no fisheye distorsion
>>>> cluster...@matrizsim <- matrizSim
>>>> cluster...@wordsinquery <- paste('"',
>>>> as.character(round(cl$centers[,1]),2),'"', '
>>>> size',as.character(cl$size))
>>>> POIcoords(clusterPOI) <- POICalc(clusterPOI
>>>> ,length(cluster...@wordsinquery))
>>>> cluster...@docs <-
>>>>
>>>> cbind(matrix(seq(1:nrow(cluster...@objeto
>>>>
>>> ))),matrix(seq(1:nrow(cluster...@objeto))))
>>
>>> cluster...@colores <- cl$cluster + 1
>>>> cluster...@cos.query.docs <- rep(1, length(cl$cluster))
>>>> POI.env <<- new.env()
>>>> POIPlot(clusterPOI)
>>>>
>>>
>>>
>>> ______________________________________________
>> 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
> Heritage Laboratories
> West Hartford, CT
>
>
>
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and provide commented, minimal, self-contained, reproducible code.
