[BioC] heatmap.2

[Jenny Drnevich]

At 02:10 PM 8/1/2007, carol white wrote:
>with greenred, I get red and black and with redgreen, I get green 
>and black. I wonder if I could have the same colors as TreeView or MapleTree.

Hi Carol,

I wouldn't say your inability to get red-black-green in your plots is 
a failure of the color schemes, but rather that your expression 
differences are almost all in one direction. You should take a 
careful look at this, and the data values that you are plotting. 
Maybe you've done an unusual transformation somewhere along the 
way?  If the expression differences are truly almost all in one 
direction, that's a warning flag that you should think about how you 
pre-processed your data and the assumptions behind the various 
methods. For example, all expression changes in one direction would 
mean that you wouldn't expect the M values in an MA plot to be 
centered on zero. I would take a very careful look at my data at all 
steps in the process to see if any mistakes have been made, or if the 
normalization steps were actually appropriate for this data set.

Jenny



>Artur Veloso <abveloso at gmail.com> wrote: Hi Carol,
>
>on the library "gplots" there is a function called "greenred" that 
>should do what I think you want to do.
>Use col=greenred(50) and see if it works out fine.
>
>Cheers,
>
>Artur
>
>On 8/1/07, carol white <wht_crl at yahoo.com> wrote:
>with col=colorRampPalette(c("red","black","green"))(256), green is 
>replaced by black and red by green, hence, red doesn't appear any more
>  At 01:18 PM 8/1/2007, carol white wrote:
>   thanks for your quick reply.
>
>  I am looking to get something closer to what is in gene expression 
> papers like  http://rana.lbl.gov/papers/Eisen_PNAS_1998.pdf  even 
> though that they use other clustering tools like TreeView. If I 
> could get almost the same red and green, it woudl be good. in this 
> heatmaps, black shows missing values or no gene expression. So I 
> don't know how to integrate this.
>  Try col=colorRampPalette(c("red","black","green"))(256)
>
>  Best,
>  Jenny
>
>
>
>  Best
>
>  Jenny Drnevich <drnevich at uiuc.edu> wrote:
>
>    Hi Carol,
>
>
>    R has 657 colors by name (see colors() ), but I don't know if 
> there is an easy way to look through them to see which of the red 
> and green options give the hues you want. However, I would caution 
> you against using a red/green scheme. I know it's used because the 
> dye colors for 2-color arrays are red and green, but for display 
> purposes red/green is a BAD choice because 10% of males are 
> red-green color blind.
>
>
>    Jenny
>
>
>    At 12:42 PM 8/1/2007, carol white wrote:
>
>    Hi,
>
>    Regarding heatmap, I would like to display the colors in green 
> and red. Is setting the parameter col in heatmap to 
> col=colorRampPalette(c("red","green"))(256) the best solution? 
> green seems to be tense and red seems to be dull (see attached).
>
>
>
>    Another solution would have been to use brewer.pal in 
> RColorBrewer package but I didn't find any name with only red and 
> green option for brewer.pal.
>
>
>    any suggestion is welcome.
>
>
>     thanks
>
>
>    carol
>
>
>
>    Building a website is a piece of cake.
>
>
>    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
>
>
>
>  Looking for a deal?  Find great prices on flights and hotels with 
> Yahoo! FareChase.
>
>
>---------------------------------
>Pinpoint customers who are looking for what you sell.
>         [[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
>
>
>
>
>
>---------------------------------
>Pinpoint customers who are looking for what you sell.
>         [[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

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