[BioC] heatmap algorithm?

James W. MacDonald jmacdon at med.umich.edu
Wed Oct 29 14:21:03 CET 2008

Hi Michaela,

These sorts of things are answered in the help pages.

?heatmap gives us:

hclustfun: function used to compute the hierarchical clustering when
           'Rowv' or 'Colv' are not dendrograms.  Defaults to 'hclust'.
           Should take as argument a result of 'distfun' and return an
           object to which 'as.dendrogram' can be applied.

and you can get more information about the hclust function at ?hclust.

Also from ?heatmap:


      Unless 'Rowv = NA' (or 'Colw = NA'), the original rows and columns
      are reordered _in any case_ to match the dendrogram, e.g., the
      rows by 'order.dendrogram(Rowv)' where 'Rowv' is the (possibly
      'reorder()'ed) row dendrogram.

So if you want a dendrogram, then no you cannot keep the original order. 
Otherwise you can.



Michaela Oswald wrote:
> Hi!
> I am new to bioconductor: what bi-clustering algorithm is behind the  
> function "heatmap"? Plus, is it possible to enforce that the order of  
> timepoints remains intact?
> Thanks, Michaela
> ###
> "A new scientific truth does not triumph by convincing its opponents  
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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