Re: [R] about col in heatmap.2

From: jim holtman <jholtman_at_gmail.com>
Date: Fri, 30 Nov 2007 20:25:14 -0500

Try this. This will plot a similar scale for data.

require(lattice)
# generate some data
x <- matrix(sample(0:8,100,replace=TRUE),10) # create 9 value # create a color palette for outpu
Lab.palette <- colorRampPalette(c("red", 'yellow','green','blue')) levelplot(x,col.regions=Lab.palette(10))

On Nov 30, 2007 7:58 PM, affy snp <affysnp_at_gmail.com> wrote:
> Hi Jim,
>
> Thanks but I imagine the transformed data would
> not actually represent the pattern from the original
> data. Is there other alternatives? Ideally, I would
> like to have the color bar looking like the one
> in http://www.bme.unc.edu/research/Bioinformatics.FunctionalGenomics.html
>
> Best,
> Allen
>
>
>
> On Nov 30, 2007 7:08 PM, jim holtman <jholtman_at_gmail.com> wrote:
> > If you are just going to have 3 values for coloring, then you could
> > just convert your data into 1, 2, 3:
> >
> > new.data <- ifelse(old.data > 2, 3, ifelse(old.data < 2, 1, 2))
> > dim(new.data) <- dim(old.data )
> >
> > and then plot it.
> >
> >
> >
> >
> > On Nov 30, 2007 5:09 PM, affy snp <affysnp_at_gmail.com> wrote:
> > > Hi list,
> > > My data set is comprised of 47 columns and about 700 rows.
> > > Most of the values would be around 2, while some will go beyond
> > > in either direction, higher or lower. Is there a way to specify the
> > > parameter of col or others if necessary to have the range of
> representing
> > > colors be 0----8, and make dark for 2, red for higher than 2 and green
> > > for lower than 2. Is there a way to do this? Thanks a lot for your
> > > suggestions.
> > >
> > > All the best,
> > > Allen
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help_at_r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > --
> > Jim Holtman
> > Cincinnati, OH
> > +1 513 646 9390
> >
> > What is the problem you are trying to solve?
> >
>
>

-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Received on Sat 01 Dec 2007 - 01:31:22 GMT

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