# Re: [R] Graphics question: How to create a changing "smudge factor" for overlapping lines?

From: Tal Galili <tal.galili_at_gmail.com>
Date: Tue, 15 Jun 2010 16:22:58 +0300

I will later cleanup the code a bit and publish it.

Best,
Tal

```#----------------------------------------

```

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)
line.width <- rep(.004, dim(Data))
Y <- NULL
X <- NULL
k.range <- 2:10

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")

centers.points <- list()

for(k in k.range)
{
cl <- kmeans(Data, k)
clusters.vec <- cl\$cluster
the.centers <- apply(cl\$centers,1, mean)

noise <- unlist(tapply(line.width, clusters.vec, cumsum))[order(seq_along(clusters.vec)[order(clusters.vec)])]  noise <- noise - mean(range(noise))
y <- the.centers[clusters.vec] + noise
Y <- cbind(Y, y)
x <- rep(k, length(y))
X <- cbind(X, x)

centers.points[[k]] <- data.frame(y = the.centers , x = rep(k , k)) # points(the.centers ~ rep(k , k), pch = 19, col = "red", cex = 1.5) }

require(colorspace)
COL <- rainbow_hcl(100)
matlines(t(X), t(Y), pch = 19, col = COL, lty = 1, lwd = 1.5)

lapply(centers.points, function(xx) {with(xx,points(y~x, pch = 19, col = "red", cex = 1.3))})

```----------------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)

On Tue, Jun 15, 2010 at 3:45 PM, Hadley Wickham <hadley_at_rice.edu> wrote:

```> the
```

> > k number of clusters, but that causes glitches in the produced image (run
```> my
```

> > code to see).
```>
> What are the glitches?  It looks pretty good to me.  (I'm not sure if
> the colour does anything apart from make it pretty though).
>
>
> --
> Assistant Professor / Dobelman Family Junior Chair
> Department of Statistics / Rice University