dendrapply: Apply a Function to All Nodes of a Dendrogram

In npcooley/SynExtend: Tools for Working With Synteny Objects

Apply a Function to All Nodes of a Dendrogram

Description

Apply function FUN to each node of a dendrogram recursively. When y <- dendrapply(x, fn), then y is a dendrogram of the same graph structure as x and for each node, y.node[j] <- FUN( x.node[j], ...) (where y.node[j] is an (invalid!) notation for the j-th node of y). Also provides flexibility in the order in which nodes are evaluated.

NOTE: This man page is for the dendrapply function defined in the SynExtend package. See ?stats::dendrapply for the default method (defined in the stats package).

Usage

dendrapply(X, FUN, ..., 
            how = c("pre.order", "post.order"))

Arguments

X	An object of class "dendrogram".
FUN	An R function to be applied to each dendrogram node, typically working on its attributes alone, returning an altered version of the same node.
...	potential further arguments passed to FUN.
how	one of c("pre.order", "post.order"), or an unambiguous abbreviation. Determines if nodes should be evaluated according to an preorder (default) or postorder traversal. See details for more information.

Details

"pre.order" preserves the functionality of the previous dendrapply. For each node n, FUN is applied first to n, then to n[[1]] (and any children it may have), then n[[2]] and its children, etc. Notably, each node is evaluted prior to any of its children.

"post.order" allows for calculations that depend on the children of a given node. For each node n, FUN is applied first to all children of n, then is applied to n itself. Notably, each node is evaluated after all of its children.

Value

Usually a dendrogram of the same (graph) structure as X. For that, the function must be conceptually of the form FUN <- function(X) { attributes(X) <- .....; X }, i.e., returning the node with some attributes added or changed.

If the function provided does not return the node, the result is a nested list of the same structure as X, or as close as can be achieved with the return values. If the function should only be applied to the leaves of X, consider using rapply instead.

Warning

dendrapply identifies leaf nodes as nodes such that attr(node, 'leaf') == TRUE, and internal nodes as nodes such that attr(node, 'leaf') %in% c(NULL, FALSE). If you modify or remove this attribute, dendrapply may perform unexpectedly.

Note

The prior implementation of dendrapply was recursive and inefficient for dendrograms with many non-leaves. This version is no longer recursive, and thus should no longer cause issues stemming from insufficient C stack size (as mentioned in the 'Warning' in dendrogram).

Author(s)

Aidan Lakshman [e-mail]

See Also

as.dendrogram, lapply for applying a function to each component of a list.

rapply is particularly useful for applying a function to the leaves of a dendrogram, and almost always be used when the function does not need to be applied to interior nodes due to significantly better performance.

Examples

require(graphics)

## a smallish simple dendrogram
dhc <- as.dendrogram(hc <- hclust(dist(USArrests), "ave"))
(dhc21 <- dhc[[2]][[1]])

## too simple:
dendrapply(dhc21, function(n) utils::str(attributes(n)))

## toy example to set colored leaf labels :
local({
  colLab <<- function(n) {
      if(is.leaf(n)) {
        a <- attributes(n)
        i <<- i+1
        attr(n, "nodePar") <- c(a$nodePar, list(lab.col = mycols[i], lab.font = i%%3))
      }
      n
  }
  mycols <- grDevices::rainbow(attr(dhc21,"members"))
  i <- 0
 })
dL <- dendrapply(dhc21, colLab)
op <- par(mfrow = 2:1)
 plot(dhc21)
 plot(dL) ## --> colored labels!
par(op)

## Illustrating difference between pre.order and post.order
dend <- as.dendrogram(hclust(dist(seq_len(4L))))

f <- function(x){
  if(!is.null(attr(x, 'leaf'))){
    v <- as.character(attr(x, 'label'))
  } else {
    v <- paste0(attr(x[[1]], 'newattr'), attr(x[[2]], 'newattr'))
  }
  attr(x, 'newattr') <- v
  x
}

# trying with default, note character(0) entries
preorder_try <- dendrapply(dend, f)
dendrapply(preorder_try, \(x){ print(attr(x, 'newattr')); x })

## trying with postorder, note that children nodes will already 
## have been populated, so no character(0) entries
postorder_try <- dendrapply(dend, f, how='post.order')
dendrapply(postorder_try, \(x){ print(attr(x, 'newattr')); x })

npcooley/SynExtend documentation built on Nov. 15, 2024, 3:02 p.m.