Re: [R] about col in heatmap.2

From: affy snp <affysnp_at_gmail.com>
Date: Fri, 30 Nov 2007 20:34:49 -0500

Jim,

This is not right as I think. The color code generated did not show a grading pattern. For example, it should go from very red---red---less red---dark----green---very green coinciding with the descending order of values, just like the very left panel shown in
http://www.bme.unc.edu/research/Bioinformatics.FunctionalGenomics.html You got my point. But the case you gave is not the case I think. Any thoughts on this? Moreover, I still prefer it be done by heatmap because I also want the dendrogram.

Best,

     Allen

On Nov 30, 2007 8:25 PM, jim holtman <jholtman_at_gmail.com> wrote:

> 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?
>

        [[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. Received on Sat 01 Dec 2007 - 01:39:12 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 03 Dec 2007 - 20:30:17 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.