Created
September 23, 2012 17:14
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From holey polygons to convex hulls
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# Highlighting clusters, with chull() | |
doInstall <- TRUE # Change to FALSE if you don't want packages installed. | |
toInstall <- c("ggplot2", "RColorBrewer") | |
if(doInstall){install.packages(toInstall, repos = "http://cran.us.r-project.org")} | |
lapply(toInstall, library, character.only = TRUE) | |
# Generate some data | |
nn <- 500 | |
myData <- data.frame(X = rnorm(nn), | |
Y = rnorm(nn)) | |
plot(myData) | |
# K-means clustering of this data | |
setK = 6 # How many clusters? | |
clusterSolution <- kmeans(myData, centers = setK) | |
myData$whichCluster <- factor(clusterSolution$cluster) | |
# One plotting approach, just colored points: | |
zp1 <- ggplot(data = myData, | |
aes(x = X, y = Y, colour = whichCluster)) | |
zp1 <- zp1 + geom_point() | |
zp1 <- zp1 + coord_equal() | |
zp1 <- zp1 + scale_colour_manual(values = colorRampPalette(rev(brewer.pal(11, "Spectral")))(setK)) | |
print(zp1) | |
# Another approach (which does not work): | |
zp2 <- ggplot(data = myData, | |
aes(x = X, y = Y, fill = whichCluster)) | |
zp2 <- zp2 + geom_polygon(alpha = 1/2) # Wow! Look at those zany polygons! | |
zp2 <- zp2 + geom_point(colour = "BLACK") | |
zp2 <- zp2 + coord_equal() | |
zp2 <- zp2 + scale_fill_manual(values = colorRampPalette(rev(brewer.pal(11, "Spectral")))(setK)) | |
print(zp2) | |
# Identify the convex hull, in three steps | |
# See also: http://www.jstatsoft.org/v40/i01/paper | |
splitData <- split(myData, myData$whichCluster) | |
appliedData <- lapply(splitData, function(df){ | |
df[chull(df), ] # chull really is useful, even outside of contrived examples. | |
}) | |
combinedData <- do.call(rbind, appliedData) | |
# do.call is useful for combining anything post-*apply | |
# Now, try the previous plot again | |
zp3 <- ggplot(data = myData, | |
aes(x = X, y = Y)) | |
zp3 <- zp3 + geom_polygon(data = combinedData, # This is also a nice example of how to plot | |
aes(x = X, y = Y, fill = whichCluster), # two superimposed geoms | |
alpha = 1/2) # from different data.frames | |
zp3 <- zp3 + geom_point(size = 1) | |
zp3 <- zp3 + coord_equal() | |
zp3 <- zp3 + scale_fill_manual(values = colorRampPalette(rev(brewer.pal(11, "Spectral")))(setK)) | |
print(zp3) |
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