Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
One of the first uses of Circos in popular print was Jonathan Corum's Naming Names graphic in the New York Times, which visualized the names used by major presidential candidates in the series of Democratic and Republican debates leading up to the Iowa caucuses.
This tutorial shows you how to create this kind of image.
Jonathan Corum describes the use of Circos for this graphic:
The circle design was created with an impressive piece of software called Circos, which was originally built to visualize genomic data. To make it work I had to encode the entire series of debates as if it was a genome. So each presidential candidate was a chromosome, and each debate was a chromosome band, and each spoken word was a nucleotide. It sounds a bit ridiculous, but that was all behind the scenes. The end result is a fairly simple interactive graphic, but hopefully one that caught the eye and allowed readers to find patterns across the long series of debates.
The most difficult part of creating a Circos image—any visualization for that matter—is deciding what data to show. Chances are your data is too complex to show (e.g. its native format doesn't have a trivial visual encoding, such as a scatter plot).
Mapping data onto a Circos figure requires that you identify what patterns in your data are (a) likely to be important and (b) likely to be present, and create a figure that exposes such patterns. Remember, if the pattern exists, you can't afford to miss it. If it doesn't exist, you can't afford to be fooled into thinking that it's there, or left wondering whether it's occluded by other data.
If you don't know where to start when creating Circos images from genomic and non-genomic data, look through published examples from the literature. Find images whose patterns map onto your data types.
Don't think necessarily from the point of view of how to construct input files. First, identify what you want to show and how. Make a sketch of the kind of figure you want to make. This is the hard part.
In the Ideograms Tutorial I have briefly mentioned that ideograms can be used to depict any axis, not just a stretch of sequence like a chromosome or contig. In this example, the segments correspond to a candidate's total word delivery during all debates.
The karyotype file defines these segments. For example, we'll say that Obama delivered 2,000 words, Richardson 1,000 words, and so on. The actual values would probably be much higher.
# karyotype.txt chr - obama obama 0 2000 dem chr - richardson richardson 0 1000 dem chr - clinton clinton 0 1500 dem chr - mccain mccain 0 1000 rep chr - romney romney 0 1750 rep chr - huckabee huckabee 0 1250 rep
The last field sets the color of the segments, according to the typical blue/red scheme for republicans and democrats. I've used the RGB values used by Jonathan.
<<include etc/colors_fonts_patterns.conf>> # append to the colors block <colors> rep = 211,121,111 dem = 85,143,190 </colors>
Each segment is divided into slices. The slice represents the number of words delivered in a specific debate.
# slices.txt obama 0 300 # Obama's 1st debate words obama 301 750 # 2nd obama 751 950 # 3rd obama 951 1250 # 4th obama 1251 1500 # 5th obama 1501 2000 # 6th
These slices are drawn as hollow highlights on top of the ideograms, with a thick white outline.
<plot> file = slices.txt type = highlight r0 = dims(ideogram,radius_inner) r1 = dims(ideogram,radius_outer) fill_color = undef stroke_color = white stroke_thickness = 5 </plot>
When a candidate mentions the name of another candidate during his speech, we draw a link. The link starts at the debate slice in which the other candidate name is mentioned. The link ends at the center of the segment of the mentioned candidate.
# links.txt # Obama mentions Clinton in his 1st debate obama 150 150 clinton 750 750 # McCain mentions Clinton in his 3rd debate mccain 875 875 clinton 750 750 # Huckabee mentions Clintin in his 2nd debate huckabee 525 525 clinton 750 750
By default, the link color is set to
rep, which is the republican red.
<link> file = links.txt radius = dims(ideogram,radius_inner) bezier_radius = 0r thickness = 5 color = rep ...
A rule is added to change the link color to
dem if the refering candidate is a democrat.
<rules> <rule> # set dem color if start is on a democrat condition = var(chr1) =~ /obama|richardson|clinton/ color = dem </rule> </rules>
To show links from a given candidate, use the
from() function which returns the name of the starting segment.
<rule> # only links from obama are shown (all others are hidden by setting show=no) # the condition test is equivalent to # var(chr1) ne "obama" condition = ! from(obama) show = no </rule>
Or, to test the identity of the segment at the end of the link, use the
<rule> # only links to mccain are shown (all others are hidden by setting show=no) # the condition test is equivalent to # var(chr2) ne "mccain" condition = ! to(mccain) show = no </rule>
fromto() function to test both ends
<rule> # only links from obama to mccain are shown (all others are hidden by setting show=no) # the condition test is equivalent to # var(chr1) ne "obama" || var(chr2) ne "mccain" condition = ! fromto(obama,mccain) show = no </rule>