From: Paul Hiemstra <p.hiemstra_at_geo.uu.nl>

Date: Wed, 16 Jun 2010 09:29:51 +0200

dat$y = dat$y + rnorm(length(dat$y), 3, 3) # Without alpha

ggplot(aes(x = x, y = y, group = grp), data = dat) + geom_line() # With alpha

ggplot(aes(x = x, y = y, group = grp), data = dat) + geom_line(alpha = 0.04, size = 2)

Date: Wed, 16 Jun 2010 09:29:51 +0200

library(ggplot2)

dat = data.frame(x = rep(1:100, 100),

y = rep(1:100, 100), grp = rep(sapply(1:100, function(x)sprintf("line%s", x)), each = 100))

dat$y = dat$y + rnorm(length(dat$y), 3, 3) # Without alpha

ggplot(aes(x = x, y = y, group = grp), data = dat) + geom_line() # With alpha

ggplot(aes(x = x, y = y, group = grp), data = dat) + geom_line(alpha = 0.04, size = 2)

cheers,

Paul

On 06/15/2010 12:57 PM, Tal Galili wrote:

> Hello all,

*>
**> I am trying to create a Clustergram in R.
**> (More about it here: http://www.schonlau.net/clustergram.html)
**>
**> And to produce a picture similar to what is seen here:
**> http://www.schonlau.net/images/clustergramexample.gif
**>
**> I was able (more or less) to write the R code for creating the image, but
**> there is one thing I can't seem to figure out, that is the
**> *changing*"smudge factor" of the lines.
**> I want the overlapping lines to "jitter" a tiny bit so they will give a
**> sense of thickness to the line (according to how many observations are
**> present in that cluster).
**> My current solution is to use a constant jitter (based on "seq") on all the
**> k number of clusters, but that causes glitches in the produced image (run my
**> code to see).
**>
**> Here is a simple self reproducible code to create the image I was able to
**> make:
**>
**>
**>
**> # ------------------------------------
**>
**> set.seed(100)
**> Data<- rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),
**> matrix(rnorm(100, mean = 1, sd = 0.3), ncol = 2))
**> colnames(x)<- c("x", "y")
**>
**> # noise<- runif(100,0,.05)
**> noise<- seq(0,.3, length.out = 100)
**> Y<- NULL
**> X<- NULL
**> k.range<- 2:10
**> for(k in k.range)
**> {
**> cl<- kmeans(Data, k)
**> y<- apply(cl$centers,1, mean)[cl$cluster] + noise
**> Y<- cbind(Y, y)
**> x<- rep(k, length(y))
**> X<- cbind(X, x)
**> points(y ~ x)
**> }
**>
**> require(colorspace)
**> COL<- rainbow_hcl(100)
**> plot(0,0, col = "white", xlim = c(1,10), ylim = c(-.5,1.6),
**> xlab = "Number of clusters", ylab = "Clusters means", main = "(Basic)
**> Clustergram")
**> axis(side =1, at = k.range)
**> abline(v = k.range, col = "grey")
**> matlines(t(X), t(Y), pch = 19, col = COL, lty = 1, lwd = 1.5)
**>
**> # The next step would be to create a method for different cluster objects,
**> but thats for another day...
**>
**>
**> #--------------------------------------------
**>
**> Any suggestions on how to do this ?
**>
**> Thanks,
**> Tal
**>
**>
**>
**> ----------------Contact
**> Details:-------------------------------------------------------
**> Contact me: Tal.Galili_at_gmail.com | 972-52-7275845
**> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
**> www.r-statistics.com (English)
**> ----------------------------------------------------------------------------------------------
**>
**> [[alternative HTML version deleted]]
**>
**> ______________________________________________
**> R-help_at_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.
**>
*

-- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 ______________________________________________ R-help_at_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.Received on Wed 16 Jun 2010 - 07:37:31 GMT

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