Re: [R] dendrogram - got it , just need to label :)
Hi!
To label your dendrogram edges with the path to each of them, execute the
following script (assuming that your dendrogram is 'dend', see last 2
lines).
dendrapplyGlobal <- function(dend,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attrName
}
funcGet <- function(x){
attr(x,attrName)
}
funcSet <- function(x,value){
attr(x,attrNameTo) <- value
return(x)
}
values <- dendrapplyToVector(dend,funcGet)
values <- FUN(values,...)
ret <- dendrapplyFromVector(dend,values,funcSet)
return(ret)
}
dendrapplyToVector <- function(X,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,path="") {
if (is.leaf(d)) {
ret <- c(FUN(d))
names(ret)[1] <- substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
ret <- vector()
for (j in seq_along(d)) {
addr <- paste(path,j,".",sep="")
ret <- append(ret,Napply(d[[j]],addr))
}
ret <- append(ret,FUN(d))
names(ret)[length(ret)] <-
substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
Napply(X)
}
dendrapplyFromVector <- function(X,theVector,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,v) {
if (is.leaf(d)) {
ret <- FUN(d,v)
return(ret)
} else {
ret <- d
if (!is.list(ret))
ret <- as.list(ret)
i <- 1
memsum <- 0
for (j in seq_along(d)) {
childrenCount <- getDendrogramNodeCount(d[[j]])
memsum <- memsum + childrenCount
indices <- i:(i+childrenCount-1)
ret[[j]] <- Napply(d[[j]],v[indices])
i <- i + childrenCount
}
ret <- FUN(ret,v[i])
}
return(ret)
}
Napply(X,theVector)
}
dend1 <- dendrapplyGlobal(dend,
"height",function(x){names(x)},attrNameTo="edgetext")
plot(dend1)
hth,
Florian
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Re: [R] accessing the "address" of items in a recursive list
j daniel wrote:
>
>
> I would like to print the "address" of the smaller dendrograms on the edge
> similar to this:
>
> addr <- function(n) {
> if(!is.leaf(n)) {
> attr(n, "edgetext") <- paste("height of",(attr(n,"height"))
> }
> n
> }
> labeledDends <- dendrapply(dend, addr)
>
> Where "i,j,k" is printed instead of "height". But I have not been able to
> figure out how to ask each dendrogram its address within the dendrapply
> function. Can anyone help me with this?
>
>
Hi!
Load the following four functions into R and execute this (assuming your
dendrogram is in variable 'dend')
newdend <- dendrapplyGlobal(dend,
"height",function(x){names(x)},attrNameTo="edgetext")
#From the specified dendrogram X a vector of all values of the specified
#node attribute is extracted, modified by the function FUN and a new
#dendrogram is created using the new values for the attribute. Optionally,
#a different attribute can be set using 'attrNameTo'
dendrapplyGlobal <- function(X,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attrName
}
funcGet <- function(x){
attr(x,attrName)
}
funcSet <- function(x,value){
attr(x,attrNameTo) <- value
return(x)
}
values <- dendrapplyToVector(X,funcGet)
values <- FUN(values,...)
ret <- dendrapplyFromVector(X,values,funcSet)
return(ret)
}
#Traverses the dendrogram in postorder and applies FUN to each node.
#The result of each evaluation is stored in the resulting array.
#Additional arguments to FUN can be passed as ...
#The names attribute of the resulting vector is the 'path' to each node.
#This implementation is based on dendrapply(graphics).
dendrapplyToVector <- function(X,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,path="") {
if (is.leaf(d)) {
ret <- c(FUN(d,...))
names(ret)[1] <- substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
ret <- vector()
for (j in seq_along(d)) {
addr <- paste(path,j,".",sep="")
ret <- append(ret,Napply(d[[j]],addr))
}
ret <- append(ret,FUN(d,...))
names(ret)[length(ret)] <-
substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
Napply(X)
}
#Traverses the dendrogram X in postorder and constructs a new dendrogram
using
#the specified function FUN and vector parVec. Each element of parVec must
#relate to a node in X, which is the case if parVec was created using
#dendrapplyToVector().
#Additional arguments to FUN can be passed as ...
#This implementation is based on dendrapply(graphics).
dendrapplyFromVector <- function(X,parVec,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,v) {
if (is.leaf(d)) {
ret <- FUN(d,v,...)
return(ret)
} else {
ret <- d
if (!is.list(ret))
ret <- as.list(ret)
i <- 1
for (j in seq_along(d)) {
childrenCount <- getDendrogramNodeCount(d[[j]])
indices <- i:(i+childrenCount-1)
ret[[j]] <- Napply(d[[j]],v[indices])
i <- i + childrenCount
}
ret <- FUN(ret,v[i],...)
}
return(ret)
}
Napply(X,parVec)
}
#Returns the number of nodes in a dendrogram.
getDendrogramNodeCount <- function(dend) {
if (!is.leaf(dend)){
childrenSum <- 0
for (child in dend) {
childrenSum <- childrenSum +
getDendrogramNodeCount(child)
}
return(childrenSum+1)
}
return(1)
}
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View this message in context:
http://www.nabble.com/accessing-the-%22address%22-of-items-in-a-recursive-list-tp13938566p15019890.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] accessing the "address" of items in a recursive list
j daniel wrote:
>
>
> I would like to print the "address" of the smaller dendrograms on the edge
> similar to this:
>
> addr <- function(n) {
> if(!is.leaf(n)) {
> attr(n, "edgetext") <- paste("height of",(attr(n,"height"))
> }
> n
> }
> labeledDends <- dendrapply(dend, addr)
>
> Where "i,j,k" is printed instead of "height". But I have not been able to
> figure out how to ask each dendrogram its address within the dendrapply
> function. Can anyone help me with this?
>
>
Hi!
Load the following four functions into R and execute this (assuming your
dendrogram is in variable 'dend')
newdend <- dendrapplyGlobal(dend,
"height",function(x){names(x)},attrNameTo="edgetext")
#From the specified dendrogram X a vector of all values of the specified
#node attribute is extracted, modified by the function FUN and a new
#dendrogram is created using the new values for the attribute. Optionally,
#a different attribute can be set using 'attrNameTo'
dendrapplyGlobal <- function(X,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attrName
}
funcGet <- function(x){
attr(x,attrName)
}
funcSet <- function(x,value){
attr(x,attrNameTo) <- value
return(x)
}
values <- dendrapplyToVector(X,funcGet)
values <- FUN(values,...)
ret <- dendrapplyFromVector(X,values,funcSet)
return(ret)
}
#Traverses the dendrogram in postorder and applies FUN to each node.
#The result of each evaluation is stored in the resulting array.
#Additional arguments to FUN can be passed as ...
#The names attribute of the resulting vector is the 'path' to each node.
#This implementation is based on dendrapply(graphics).
dendrapplyToVector <- function(X,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,path="") {
if (is.leaf(d)) {
ret <- c(FUN(d,...))
names(ret)[1] <- substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
ret <- vector()
for (j in seq_along(d)) {
addr <- paste(path,j,".",sep="")
ret <- append(ret,Napply(d[[j]],addr))
}
ret <- append(ret,FUN(d,...))
names(ret)[length(ret)] <-
substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
Napply(X)
}
#Traverses the dendrogram X in postorder and constructs a new dendrogram
using
#the specified function FUN and vector parVec. Each element of parVec must
#relate to a node in X, which is the case if parVec was created using
#dendrapplyToVector().
#Additional arguments to FUN can be passed as ...
#This implementation is based on dendrapply(graphics).
dendrapplyFromVector <- function(X,parVec,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,v) {
if (is.leaf(d)) {
ret <- FUN(d,v,...)
return(ret)
} else {
ret <- d
if (!is.list(ret))
ret <- as.list(ret)
i <- 1
for (j in seq_along(d)) {
childrenCount <- getDendrogramNodeCount(d[[j]])
indices <- i:(i+childrenCount-1)
ret[[j]] <- Napply(d[[j]],v[indices])
i <- i + childrenCount
}
ret <- FUN(ret,v[i],...)
}
return(ret)
}
Napply(X,parVec)
}
#Returns the number of nodes in a dendrogram.
getDendrogramNodeCount <- function(dend) {
if (!is.leaf(dend)){
childrenSum <- 0
for (child in dend) {
childrenSum <- childrenSum +
getDendrogramNodeCount(child)
}
return(childrenSum+1)
}
return(1)
}
hth,
Florian
--
View this message in context:
http://www.nabble.com/accessing-the-%22address%22-of-items-in-a-recursive-list-tp13938566p15019892.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
