[BioC] heatmap.2
Matthias.Kohl at stamats.de
Matthias.Kohl at stamats.de
Thu Aug 2 06:21:14 CEST 2007
Hi,
I implemented a little function in my R package SLmisc which can help to adjust the colors;
see
library(SLmisc)
example(heatmapCol)
Best,
Matthias
----- original message --------
Subject: Re: [BioC] heatmap.2
Sent: Wed, 01 Aug 2007
From: carol white<wht_crl at yahoo.com>
> back to standardization discussion, is it better to do
> 1- mean centering, or
> 2- median centering of variables or
> 3- mean = 0, standard deviation = 1 of variables?
>
> 1 and 2 could be done with scale function (center = T). so we would know
> what the results would be.
>
> Jenny Drnevich <drnevich at uiuc.edu> wrote: Hi,
>
> I prefer not to standardize around 0 or use the
> scale="row" option of heatmap2, because it's not
> always clear what the resulting values mean. What
> I've done is to add a row to the data to force the center to be on zero:
>
> > class(mean.sig.05)
> [1] "matrix"
>
> > dim(mean.sig.05)
> [1] 101 15
>
> > max(mean.sig.05)
> [1] 3.24023
>
> > min(mean.sig.05)
> [1] -3.120530
>
> > mean.sig.05 <- rbind(mean.sig.05,fake=c(3.24,rep(0,13),-3.24))
>
> > rownames(mean.sig.05) <- NULL
>
> >hmcol2 <- colorRampPalette(c("red","white","blue"))(256)
>
> > heatmap_2(mean.sig.05,col=hmcol2,legend=1,do.dendro=c(T,T),scale="none")
>
> Of course, it's not ideal to have a faked row of
> data in the plot, but it doesn't really show if you have >50 genes.
>
> Cheers,
> Jenny
>
> At 06:24 AM 8/1/2007, Benjamin Otto wrote:
> >How about data standardization before plotting? Should center the values
> >automatically around 0. There is some flag in the function to da that,
> >but I don't have it in mind right now.
> >
> >regards,
> >
> >Benjamin
> >
> >
> >Am Dienstag, den 31.07.2007, 09:56 +0200 schrieb Kauer Maximilian Otto:
> > > Dear list,
> > >
> > > Is there a way to force the colors in
> > heatmap.2 to center on 0 i.e to to force 0 to
> > be white even though the spread in the data is
> > unequal (say -7 to +4)? I'm using bluered, but could use different color
> sets.
> > >
> > > Thank You,
> > > Max
> > >
> > > _______________________________________________
> > > 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
> > >
> >
> >
> >
> >--
> >Pflichtangaben gemäß Gesetz über elektronische
> >Handelsregister und Genossenschaftsregister
> >sowie das Unternehmensregister (EHUG):
> >
> >Universitätsklinikum Hamburg-Eppendorf
> >Körperschaft des öffentlichen Rechts
> >Gerichtsstand: Hamburg
> >
> >Vorstandsmitglieder:
> >Prof. Dr. Jörg F. Debatin (Vorsitzender)
> >Dr. Alexander Kirstein
> >Ricarda Klein
> >Prof. Dr. Dr. Uwe Koch-Gromus
> >
> >
> >_______________________________________________
> >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
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
> _______________________________________________
> 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
>
>
>
> Jenny Drnevich <drnevich at uiuc.edu> wrote: Hi,
>
> I prefer not to standardize around 0 or use the
> scale="row" option of heatmap2, because it's not
> always clear what the resulting values mean. What
> I've done is to add a row to the data to force the center to be on zero:
>
> > class(mean.sig.05)
> [1] "matrix"
>
> > dim(mean.sig.05)
> [1] 101 15
>
> > max(mean.sig.05)
> [1] 3.24023
>
> > min(mean.sig.05)
> [1] -3.120530
>
> > mean.sig.05 <- rbind(mean.sig.05,fake=c(3.24,rep(0,13),-3.24))
>
> > rownames(mean.sig.05) <- NULL
>
> >hmcol2 <- colorRampPalette(c("red","white","blue"))(256)
>
> > heatmap_2(mean.sig.05,col=hmcol2,legend=1,do.dendro=c(T,T),scale="none")
>
> Of course, it's not ideal to have a faked row of
> data in the plot, but it doesn't really show if you have >50 genes.
>
> Cheers,
> Jenny
>
> At 06:24 AM 8/1/2007, Benjamin Otto wrote:
> >How about data standardization before plotting? Should center the values
> >automatically around 0. There is some flag in the function to da that,
> >but I don't have it in mind right now.
> >
> >regards,
> >
> >Benjamin
> >
> >
> >Am Dienstag, den 31.07.2007, 09:56 +0200 schrieb Kauer Maximilian Otto:
> > > Dear list,
> > >
> > > Is there a way to force the colors in
> > heatmap.2 to center on 0 i.e to to force 0 to
> > be white even though the spread in the data is
> > unequal (say -7 to +4)? I'm using bluered, but could use different color
> sets.
> > >
> > > Thank You,
> > > Max
> > >
> > > _______________________________________________
> > > 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
> > >
> >
> >
> >
> >--
> >Pflichtangaben gemäß Gesetz über elektronische
> >Handelsregister und Genossenschaftsregister
> >sowie das Unternehmensregister (EHUG):
> >
> >Universitätsklinikum Hamburg-Eppendorf
> >Körperschaft des öffentlichen Rechts
> >Gerichtsstand: Hamburg
> >
> >Vorstandsmitglieder:
> >Prof. Dr. Jörg F. Debatin (Vorsitzender)
> >Dr. Alexander Kirstein
> >Ricarda Klein
> >Prof. Dr. Dr. Uwe Koch-Gromus
> >
> >
> >_______________________________________________
> >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
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
> _______________________________________________
> 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
>
>
>
> ---------------------------------
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>
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>
>
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