[BioC] heatmap algorithm?
James W. MacDonald
jmacdon at med.umich.edu
Wed Oct 29 14:21:03 CET 2008
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:
> 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
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James W. MacDonald, M.S.
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