[R] heatmap help

[Marta Rufino]

Hello,


I was just doing heatmaps myself ;-) and I had the same problem. It would be
nice to have such an example in the help file because it is not clear (thank
you).
you use (for example... this is my case, which I am doing the distance
matrix using vegdist function with Bray curtis similarity):

heatmap(matrix, scale="none", distfun=function(m) vegdist(m, method="bray"),
hclustfun=function(m) hclust(m, method="average"), col=
grey(seq(0.8,0,l=5)))

or you can put directly the distance matrix that you may want, but I found
it worst. To have the right labels on I found that the best way would be to
have them in the matrix directely, because if we put it after it does not
work well...

I have been having difficulties in producing the scale that I want and doing
the correct legend...
I found an email with a function (image.scale()), but it does not work
entirely well.
How can I define the values I want in the scale, for example, use red for 1
g, blue for 2 g, etc...
Is there a simpler way of doing the legend?

thank you very much,
Marta


> Dear R wizards,
> Hopeful someone can help me with what I believe is a pretty simple task.
I
> pretty new to R so some (much) of the obvious escapes me. How do I get a
> distance matrix into heatmap?  What do I tell distfun if what I'm trying
to
> map is already an ordered distance matrix?  I tried >heatmap(x,
> distfun=as.dist(x)) where x is the distance matrix but R gave me an error.
> Thanks in advance for any help.
>
> Paul Lepp
>
>  `-:-.   ,-;"`-:-.   ,-;"`-:-.   ,-;"`-:-.   ,-;"`-:-.   ,-;"`-:-.
>    `=`,'=/     `=`,'=/     `=`,'=/     `=`,'=/     `=`,'=/     `=`
>      >==/        >==/        >==/        >==/        >==/
>    ,=,-<=`.    ,=,-<=`.    ,=,-<=`.    ,=,-<=`.    ,=,-<=`.    ,=,
> ,-'-'   `-=_,-'-'   `-=_,-'-'   `-=_,-'-'   `-=_,-'-'   `-=_,-'-'
> Paul Lepp, Ph.D.                       Stanford School of Medicine
>
> VAPAHCS, 154T                   Dept. of Microbiology & Immunology
> 3801 Miranda Ave                               Stanford University
> Palo Alto, CA 94304                                   Stanford, CA
> (650) 493-5000 x66762                fax: (650) 852-3291
> http://cmgm.stanford.edu/~pwlepp          pwlepp at cmgm.stanford.edu
>
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