I don't quite get what kind of cloudness Alyaa have. If it is about margin.
the parameters margin, lhei might help.

Wenhuo
On Apr 11, 2012 8:40 AM, "Alyaa Mahmoud" <alyamahmoud@gmail.com> wrote:

> Dear all
>
> I use heatmap.2 to generate a heatmap, but the generated pdf seems very
> cloudy !!! I use the following lines of code,
> can anyone help allocate where the problem is ??
>
> # generate heatmap for matrix bb
> hc <- hclust(as.dist(1-cor(as.matrix(bb), method="spearman")),
> method="complete", members=NULL)
> # Clusters columns by Spearman correlation as distance method.
> hr <- hclust(as.dist(1-cor(t(as.matrix(bb)), method="spearman")),
> method="complete", members=NULL)
>
> mycl <- cutree(hr, h=max(hr$height)/1.5);
> mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9);
> mycolhc <- mycolhc[as.vector(mycl)] # Cuts the tree and creates color
> vector for clusters.
>
> library(gplots);
> myheatcol <- redgreen(75)
> pdf("heatmap_dataset1.pdf")
> heatmap.2(bb, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc),
> col=myheatcol, scale="row", density.info="none", trace="none",
> RowSideColors=mycolhc)
> dev.off()
>
>
> Thanks a lot
> yours,
> Alyaa
>
> --
> Alyaa Mahmoud
>
> "Love all, trust a few, do wrong to none"- Shakespeare
>
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>
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