[BioC] Heatmap without using clustering result

[Laurent Gautier]

Wolfgang Huber wrote:
> Hi Gregory
> 
> "levelplot" in the "lattice" package is a better alternative to
> "graphics::image" (however, as far as I know, and I'd love to be
> corrected, it does not easily integrate into layouts of multiple panels).

It integrates as good as other lattice plots, I would say (and the claim 
of simplicity is left for an other time).

May be I just do not see how it wouldn't and you'd have an example of 
what can't be done ?


> For straightforward image display, "display" in "EBImage" (please use
> the development version,
> http://www.bioconductor.org/packages/devel/bioc/html/EBImage.html) can
> be efficient.
> 
> "heatmap.2" in the "gplots" package is a better alternative to
> "stats::heatmap".
> 
> For even more flexible reordering of rows and columns, have a look at
> the example of the "dendrogramGrob" function in the "latticeExtra" package.
> 
> 	Best wishes
> 	Wolfgang
> 
> 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> 
> 
> 
> 25/02/2009 23:59 Steve Pederson scripsit
>> Hi Greg,
>>
>> heatmap() is essentially a call to image() so try image(t(your.data)). I
>> found you can get nice control over the colours & the overall appearance
>> this way, although it does take a bit more messing around.
>>
>> Cheers,
>>
>> Steve
>>
>>
>> gregory voisin wrote:
>>> Hie,
>>> I use heatmap() for expression data.
>>> my data set is already ordered by Mfuzz clustering.
>>>
>>> If I use  my heatmap on my ordered.data.set, I get a beautiful heatmap
>>> reclustering by hclust.
>>>  
>>> by consequently, I have 2 possibility.
>>> 1. desactive hclust () in heatmap(): like this , I get a heatmap of my
>>> ordered.data.set without ordering by hclust()
>>>
>>> 2. integrate mfuzz, in heatmap function ( heatmap ( eset, hclust =
>>> function(x) mfuzz)
>>>
>>> After severals tries et prospection on Internet, I need your help
>>>
>>> Greg
>>>
>>>
> 
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