Larger values masking others for OmicCircos heatmap

Question

[Peter.Wood]

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);

Answer 1

[Irsan]

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