hclust_rect {MethylIT.utils}R Documentation

Draw Rectangles with Background Colors Around Hierarchical Clusters


Draws rectangles with background colors around the branches of a dendrogram highlighting the corresponding clusters. First the dendrogram is cut at a certain level, then a rectangle is drawn around selected branches.


hclust_rect(tree, k = NULL, which = NULL, x = NULL, h = NULL,
  border = 2, cluster = NULL, cuts = NULL, color = NULL, ...)



The same as in rect.hclust

k, h

The same as in rect.hclust

which, x

The same as in rect.hclust


The same as in rect.hclust


The same as in rect.hclust


A numeric vector used to manually locate the rectangles around hierarchical clusters in the rigth position. This is tricky since each experimental dataset yield different measurement scale and must be manually adjusted. Settings are cuts = c(xleft, ybottom, xright, ytop). Default is NULL. Use it only if need it.


Background color to use inside the rectangles around hierarchical clusters. Default is NULL.


This function is exactly function rect.hclust with a nice feature added: "to draw the rectangles around hierarchical clusters with background colors".


### Violent crime rates by US state
hca <- hclust(dist(USArrests))

# Basic key RGB colors
# rgb(red, green, blue, alpha, names = NULL, maxColorValue = 1)
clusters.color = c(rgb(0, 0.7, 0, 0.1), rgb(0, 0, 1, 0.1),
                 rgb(1, 0.2, 0, 0.1))

hclust_rect(hca, h = 150,  border = clusters.color, col = clusters.color )

[Package MethylIT.utils version 0.3.2 ]