Colored dendrogram

This function plot an dendrogram with different colors to each cluster for a given number of classes. See examples.

A2Rplot(
  x,
  k = 2,
  col.up = "black",
  col.down = rainbow(k),
  lty.up = 2,
  lty.down = 1,
  lwd.up = 1,
  lwd.down = 2,
  type = c("rectangle", "triangle"),
  knot.pos = c("mean", "bary", "left", "right", "random"),
  criteria,
  fact.sup,
  show.labels = TRUE,
  only.tree = FALSE,
  main = paste("Colored Dendrogram (", k, " groups)"),
  boxes = TRUE,
  members
)

Source

http://addictedtor.free.fr/packages/A2R/lastVersion/

Arguments

x

an hclust object to plot

k

the number of clusters

col.up

color for the upper part

col.down

a vector of colors of length k, one color per cluster

lty.up

line type for the upper part (see par)

lty.down

line type for the clusters part (see par)

lwd.up

line width for the upper part (see par)

lwd.down

line width for the clusters part (see par)

type

type of link ("rectangle" or "triangle")

knot.pos

position of the knots: "mean" mean between the two tree sons, "bary" weighted mean relative to the number of observations in the left and the right branch, "left", "right", "random" just for fun actually

criteria

vector of a criteria to draw on the left of the tree

fact.sup

a factor to categorize the observations

show.labels

TRUE if the labels should be drawn

only.tree

TRUE if only the tree should be drawn (use that to include the tree in a more complicated layout)

main

title of the plot

boxes

TRUE to draw the bow around the plots

members

members of each terminal node (see hclust for more details)

Note

The A2R package has not been updated since January 2006 and cannot be installed anymore with a recent version of R. It's why this function has been copied here.

See also

http://rpubs.com/gaston/dendrograms, plot.hclust

Author

Romain Francois

Examples

# Example with iris data
d <- dist(iris[, 1:4], method = "euc")
h <- hclust(d)
Species <- iris[, 5]
A2Rplot(h, k = 3, fact.sup = Species, knot.pos = "bary", show.labels = FALSE)


# Examples from http://rpubs.com/gaston/dendrograms

bg.def <- par()$bg

hc <- hclust(dist(mtcars))
par(bg = "#EFEFEF")
A2Rplot(hc,
  k = 3, boxes = FALSE, col.up = "gray50",
  col.down = c("#FF6B6B", "#4ECDC4", "#556270")
)


par(bg = "gray15")
cols <- hsv(c(0.2, 0.57, 0.95), 1, 1, 0.8)
A2Rplot(hc, k = 3, boxes = FALSE, col.up = "gray50", col.down = cols)


par(bg = bg.def)

# Examples with state.x77
d77 <- dist(state.x77)
h77 <- hclust(d77)
A2Rplot(h77, k = 4, knot.pos = "mean", type = "tri")

A2Rplot(h77,
  k = 4, lty.up = 1, lwd.down = 1,
  col.down = c("purple", "black", "green3", "orange"),
  col.up = "gray", boxes = FALSE
)


A2Rplot(h77, k = 4, knot.pos = "left", type = "tri")


# Example showing how to include this in an other layout with only.tree
op <- par(no.readonly = TRUE)
par(mfrow = c(3, 3))
par(mar = c(3, 3, 3, 3))
plot(rnorm(50)) # one plot
plot(rnorm(50)) # one plot
plot(rnorm(50)) # one plot
plot(rnorm(50)) # one plot
par(mar = c(1, 1, 1, 1))
A2Rplot(h77, k = 4, only.tree = TRUE, boxes = FALSE)
#> NULL
par(mar = c(3, 3, 3, 3))
plot(rnorm(50)) # one plot
plot(rnorm(50)) # one plot
plot(rnorm(50)) # one plot
plot(rnorm(50)) # one plot

par(op)

# Example using members
hc <- hclust(dist(USArrests)^2, "cen")
memb <- cutree(hc, k = 10)
cent <- NULL
for (k in 1:10) {
  cent <- rbind(cent, colMeans(USArrests[memb == k, , drop = FALSE]))
}
hc1 <- hclust(dist(cent)^2, method = "cen", members = table(memb))
hc1$labels <- paste("g", 1:10)
A2Rplot(hc1,
  members = table(memb),
  k = 4,
  lwd.up = 2, lty.up = 1, col.up = "gray",
  lwd.down = 1, lty.down = "twodash",
  col.down = c("orange", "brown", "green3", "royalblue"),
  knot.pos = "bary"
)