[R] hclust in heatmap.2

[affy snp]

Dear list,

I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix
x clustered only by columns and keep the original order of rows unchanged.
Is there a way to do that in heatmap.2()?

Thanks a lot! Any suggestions will be appreciated!

Best,
Allen

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[Ashoka Polpitiya]

Check the Rowv, Colv options to heatmap.2

data(mtcars)
x <- as.matrix(mtcars)
heatmap.2(x, Rowv=FALSE, dendrogram="column")

-Ashoka
----
Scientist - Pacific Northwest National Lab

[James W. MacDonald]

affy snp wrote:
> Dear list,
>
> I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix
> x clustered only by columns and keep the original order of rows unchanged.
> Is there a way to do that in heatmap.2()?
>
> Thanks a lot! Any suggestions will be appreciated!

From the help page:

Arguments:

x: numeric matrix of the values to be plotted.

Rowv: determines if and how the _row_ dendrogram should be
reordered. By default, it is TRUE, which implies dendrogram
is computed and reordered based on row means. If NULL or
FALSE, then no dendrogram is computed and reordering is done.
If a 'dendrogram', then it is used "as-is", ie without any
reordering. If a vector of integers, then dendrogram is
computed and reordered based on the order of the vector.

>
> Best,
> Allen
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-h...@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.

--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

[affy snp]

Thanks Ashoka!

Allen

On Dec 6, 2007 12:27 AM, Ashoka Polpitiya <ashoka.p...@gmail.com>
wrote:

[affy snp]

Thanks James!

Allen