[BioC] hclustfun argument in heatmap.2 function

[James W. MacDonald]

Hi Carol,

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"

The argument hclustfun expects you to pass a function name, not the 
output from calling the function you want to use (which is what you are 
doing).

 > myfun <- function(x) hclust(as.dist(1-cor(t(as.matrix(x)), method = 
"pearson")), method = "average")
 > heatmap.2(as.matrix(mtcars), dendrogram = "none", hclustfun = myfun)

Best,

Jim


> 
> 
> 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]]
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826