Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
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Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong from the Points of View series.
Before I get into local scale adjustment in the next tutorial, I want to cover a simple way to adjust the scale in a region of an ideogram.
In this example, I have drawn 0-60 Mb regions of chromosomes 1 and 2, by breaking them up into three regions each. The resulting image has 6 ideograms, 3 per chromosome. Using chromosomes_scale, the scale for the ideograms is adjusted like in the previous example.
chromosomes = hs1[a]:0-20;hs2[b]:0-20;hs1[c]:20-40;hs2[d]:20-40;hs1[e]:40-60;hs2[f]:40-60 chromosomes_scale = a:0.5;b:0.5;e:5;f:5
Note that ideogram tags (a, b, c, ...) are required because we have multiple idoegrams per chromosome and it is not sufficient to use the chromosome name to uniquely specify an ideogram.
For example, if you would like to expand (or contract) the scale on a specific region of an ideogram using global scale adjustment, break the ideogram into multiple region that demarcate your region of interst and apply a new scale to the region. For example, here's a way to zoom in on the 50-60Mb region on chr1 by 10x.
chromosomes = hs1[a]:0-50;hs1[b]:50-60;hs1[c]:60-) chromosomes_scale = b:10
Note the 60-) syntax in the chromosome range field. This means from 60 to the end of the chromosome, and saves you remembering the exact size of the chromosome. The size of each chromosome is defined in the karyotype file.