Question: Larger values masking others for OmicCircos heatmap
0
gravatar for Peter.Wood
5.5 years ago by
Peter.Wood0
Australia
Peter.Wood0 wrote:

I am wondering whether the heatmap scale for the circos plot can be specified to each gene. At the moment the  highly expressed genes are masking the others so that differential expression patterns are not being shown for all of the genes.


 circos(R=110, cir=db, W=200, mapping=gene.expression,  col.v=4,  type="heatmap2", col.bar=T, lwd=1);
ADD COMMENTlink modified 5.5 years ago by Irsan7.2k • written 5.5 years ago by Peter.Wood0
1
gravatar for Irsan
5.5 years ago by
Irsan7.2k
Amsterdam
Irsan7.2k wrote:

This is a common problem and can be solved by scaling your expression matrix by rows. So make Z-scores of your matrix by rows. Assuming you have samples in columns and genes in rows in an object called data you can do this in R by

scaledData <- t(scale(t(data)) 

This way you don't have to define color-value mappings per gene

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Irsan7.2k
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