[R] problem building dendrograms to use with heatmap()

[Paul Murrell]

Hi


Wittner, Ben wrote:
> Hi,
> 
> I'm trying to build dendrograms to pass to heatmap().
> The dendrograms I build plot properly, but when I pass them to heatmap() I get
> the error message "row dendrogram ordering gave index of wrong length" (see
> output log below).


Looks like you're not building the dendrograms "properly".  Compare 
unclass(nr2) with unclass() of a dendrogram from 
as.dendrogram(hclust(<something>)).  You might need to look closely at 
stats:::as.dendrogram.hclust to get it right.

Paul


> I looked in the code of heatmap() and saw that the error was due to a NULL
> return value from order.dendrogram(), which in turn got a NULL return value from
> unlist(). But I have no idea why unlist() is returning NULL.
> 
> I've included code below which reproduces the problem and below that the output
> from a run of that code on my computer.
> 
> Any help would be greatly appreciated. Thanks in advance.
> 
> -Ben
> 
> ###########################  begin code  ###################################
> 
> version
> 
> dendro.leaf <- function(label) {
>   ans <- list()
>   attr(ans, 'members') <- 1
>   attr(ans, 'height') <- 0
>   attr(ans, 'leaf') <- T
>   attr(ans, 'midpoint') <- 0
>   attr(ans, 'label') <- label
>   attr(ans, 'class') <- 'dendrogram'
>   ans
> }
> 
> dendro.merge <- function(d1, d2, height) {
>   ans <- list(d1, d2)
>   members <- attr(d1, 'members') + attr(d2, 'members')
>   attr(ans, 'members') <- members
>   attr(ans, 'height') <- height
>   attr(ans, 'leaf') <- F
>   attr(ans, 'midpoint') <- (members - 1)/2
>   attr(ans, 'class') <- 'dendrogram'
>   ans
> }
> 
> lc1 <- dendro.leaf('c1')
> lc2 <- dendro.leaf('c2')
> lc3 <- dendro.leaf('c3')
> nc1 <- dendro.merge(lc1, lc2, 0.1)
> nc2 <- dendro.merge(nc1, lc3, 0.2)
> plot(nc2)
> 
> lr1 <- dendro.leaf('r1')
> lr2 <- dendro.leaf('r2')
> lr3 <- dendro.leaf('r3')
> nr1 <- dendro.merge(lr2, lr3, 0.1)
> nr2 <- dendro.merge(lr1, nr1, 0.3)
> plot(nr2)
> 
> x <- matrix(seq(-1, 1, length.out=9), nrow=3)
> rownames(x) <- paste('r', 1:3, sep='')
> colnames(x) <- paste('c', 1:3, sep='')
> 
> heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
> 
> order.dendrogram(nr2)
> 
> unlist(nr2)
> 
> ###############  begin output from run of code above  ##################
> 
> 
>>version
> 
>          _                
> platform i686-pc-linux-gnu
> arch     i686             
> os       linux-gnu        
> system   i686, linux-gnu  
> status                    
> major    2                
> minor    1.1              
> year     2005             
> month    06               
> day      20               
> language R                
> 
>>dendro.leaf <- function(label) {
> 
> +   ans <- list()
> +   attr(ans, 'members') <- 1
> +   attr(ans, 'height') <- 0
> +   attr(ans, 'leaf') <- T
> +   attr(ans, 'midpoint') <- 0
> +   attr(ans, 'label') <- label
> +   attr(ans, 'class') <- 'dendrogram'
> +   ans
> + }
> 
>>dendro.merge <- function(d1, d2, height) {
> 
> +   ans <- list(d1, d2)
> +   members <- attr(d1, 'members') + attr(d2, 'members')
> +   attr(ans, 'members') <- members
> +   attr(ans, 'height') <- height
> +   attr(ans, 'leaf') <- F
> +   attr(ans, 'midpoint') <- (members - 1)/2
> +   attr(ans, 'class') <- 'dendrogram'
> +   ans
> + }
> 
>>lc1 <- dendro.leaf('c1')
>>lc2 <- dendro.leaf('c2')
>>lc3 <- dendro.leaf('c3')
>>nc1 <- dendro.merge(lc1, lc2, 0.1)
>>nc2 <- dendro.merge(nc1, lc3, 0.2)
>>plot(nc2)
>>
>>lr1 <- dendro.leaf('r1')
>>lr2 <- dendro.leaf('r2')
>>lr3 <- dendro.leaf('r3')
>>nr1 <- dendro.merge(lr2, lr3, 0.1)
>>nr2 <- dendro.merge(lr1, nr1, 0.3)
>>plot(nr2)
>>
>>x <- matrix(seq(-1, 1, length.out=9), nrow=3)
>>rownames(x) <- paste('r', 1:3, sep='')
>>colnames(x) <- paste('c', 1:3, sep='')
>>
>>heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
> 
> Error in heatmap(x, Rowv = nr2, Colv = nc2, scale = "none") : 
>         row dendrogram ordering gave index of wrong length
> 
>>order.dendrogram(nr2)
> 
> NULL
> 
>>unlist(nr2)
> 
> NULL
> 
> 
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-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/