Circos plot heatmap
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6.2 years ago
Peter.Wood • 0

In the Circos plot, the heatmap is distorted by extreme values by certain genes. I am inquiring whether the heatmap can be applied independently to each gene that  will allow me to view the gene expression between each experiment groups for every gene.


 par(mar=c(2, 2, 2, 2));

 plot(c(1,800), c(1,800), type="n", axes=F, xlab="", ylab="", main="");

circos(R=300, cir=db, W=4,   type="chr", print.chr.lab=T, col=cols);
circos(R=110, cir=db, W=200, mapping=gene.expression,  col.v=4,  type="heatmap2", col.bar=T, lwd=1);
circos(R=310, cir=db, W=20,  mapping=gene.expression, type="label", side="out", col="black");
differential gene expression heatmap • 3.9k views
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doesn't the last example of the circos vignette shows a heatmap for each gene separately inside the circle?

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The line

circos(R=110, cir=db, W=200, mapping=gene.expression,  col.v=4,  type="heatmap2", col.bar=T, lwd=1);

generates a heatmap, but its scale is universal for every gene plotted with the extreme values of some genes masking the other gene expression patterns.

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you can try and manually change the variables in the circos command. Lines 2119-2120 of the circos command are the two giving the max and min values for the heatmap by taking the maximum and minimum of the matrix of expression values you're working with. If you'll manually set this to a different value, you'll get a different distribution of the data
 

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