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Question: Heatmap without using clustering result
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gravatar for gregory voisin
8.7 years ago by
Canada
gregory voisin430 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 [[alternative HTML version deleted]]
ADD COMMENTlink modified 8.7 years ago by Steve Pederson60 • written 8.7 years ago by gregory voisin430
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gravatar for michael watson IAH-C
8.7 years ago by
michael watson IAH-C3.4k wrote:
Set both Rowv and Colv arguments to NULL and this should turn off clustering and just draw the heatmap -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of gregory voisin Sent: Wed 25/02/2009 9:56 PM To: bioconductor Subject: [BioC] Heatmap without using clustering result 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 8.7 years ago by michael watson IAH-C3.4k
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gravatar for Steve Pederson
8.7 years ago by
Steve Pederson60 wrote:
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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.7 years ago by Steve Pederson60
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). 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 >> >>
ADD REPLYlink written 8.7 years ago by Wolfgang Huber13k
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 >>> >>> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 8.7 years ago by Laurent Gautier2.2k
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