[BioC] hclustfun argument in heatmap.2 function

[Joern Toedling]

Hello,

that's because the argument hclustfun really expects a function (as does
distfun), but you supply the result of the hierarchical clustering to this
argument.

Try the following way:

hclust2 <- function(x, method="average", ...)
  hclust(x, method=method, ...)
dist2 <- function(x, ...)
  as.dist(1-cor(t(x), method="pearson"))

heatmap.2(as.matrix(mtcars), distfun=dist2, hclustfun=hclust2, <your other
arguments here>)

Regards,
Joern

PS: your R is very outdated, please upgrade to the current release version
(2.9.1). And actually the package gplots is not a Bioconductor package, so
maybe this list is not the right place to post such questions.


On Fri, 31 Jul 2009 04:43:04 -0700 (PDT), carol white wrote
> Hi,
> When using hclustfun argument in heatmap.2 function, I get the error 
> message below. Note that I want to use average linkage with pearson correlation.
> 
>  heatmap.2(as.matrix(mtcars), dendrogram = "none", hclustfun  = 
> hclust(as.dist(1-cor(t(as.matrix(mtcars)), method = "pearson"))
> ,method = "average")) Error in heatmap.2(as.matrix(mtcars),
>  dendrogram = "none", hclustfun = hclust(as.dist(1 -  :     could 
> not find function "hclustfun"
> 
> I use the R version
>           
> > version     _                           
> platform       x86_64-redhat-linux-gnu     
> arch           x86_64                      
> os             linux-gnu                   
> system         x86_64, linux-gnu           
> status                                     
> major          2                           
> minor          5.1                         
> year           2007                        
> month          06                          
> day            27                          
> svn rev        42083                       
> language       R                           
> version.string R version 2.5.1 (2007-06-27)
> 
> thanks,
> 
> 	[[alternative HTML version deleted]]


---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246926