On This Page:
Circos is a visualization tool created by Martin Krzywinski from the Michael Smith Genome Sciences Centre of Canada. Circos is a powerful command line tool that is particularly well suited for visualizing comparative genomics data, such as alignments, conservation and duplication events. Circos also supports drawing generalized 2D data in the form of line plots, scatter plots, heatmaps and histograms. Unlike other visualization tools, Circos conveys information by drawing circular ideograms, which makes it extremely valuable for displaying intra- and inter-chromosomal relationships. Circos is similar to other circular visualization tools such as chromowheel or genopix. However, Circos' extremely flexible engine allows the user significant control and customization opportunities that can result in publication-quality, aesthetically pleasing images.
Circos has an extensive variety of tutorials and tutorial images which provide information regarding the capabilities of Circos and the available options for creating images. Circos has also been published: Circos: an Information Aesthetic for Comparative Genomics.
The Circos User Interface (UI) was created to provide users with a simple way to use this powerful command-line tool. Currently, the provided Circos UI supports options for the version 0.51-1 release. Circos is an extremely powerful and flexible tool that can respond to a large number of options and customizations. While the available options in the UI allow a user a high level of control over the resulting image, further options have been left out for simplicity. Please keep in mind that while visiting the Circos webpage and viewing the available tutorials, not all options discussed will be available in the interface. However, after running Circos, you will be able to download all necessary configuration files for your Circos run. If you would like to install Circos on your local machine, you can alter your downloaded configuration file to explore those other options.
The Circos UI provides a wizard-like interface for configuring a run of Circos. Each tab can be traversed in order by clicking the Next Step and Previous Step buttons. However visiting each tab is not required to configure Circos. If you are familiar with the Circos UI and know exactly which tab to visit to customize your desired option you can go directly to the tab by clicking on the tab title.
10.2. Entry Points
On the Select Entry Points tab, a user can specify which entry points should be drawn in the image and also modify the appearance of entry points. Circos images comprise a circular representation of entry points with data tracks that can be drawn inside or outside of the circular composition. The symbolic representation of the entry points are called ideograms. In the Genboree context, a Circos ideogram can be thought of as the physical representation of an entry point.
NOTE: At least one entry point must be selected for drawing
10.2.1. Global Entry Points Properties
In the Specification for All Entry Points section, the user can set properites that will be applied to all entry points that are drawn in the image. The options that can be collectively specified for all entry points are describe below.
Draw entry point labels:
Enable/disable the drawing of entry point labels. Entry point labels alert the user to which entry point they are viewing in the resulting image.
Draw cytogenetic banding:
Cytogenetic bands can be drawn on top of the entry points. Upon enabling cytogenetic banding, a list of all annotation tracks will appear. Select the annotation track that contains the banding information
NOTE: Only tracks that contain the Genboree attribute-value pair (AVP), bandType will display the typical banding color scheme. If a track without the bandType fiels is specified, the bands will be outlined on the entry point.
Color entry points:
Specify a color to fill each entry point. After enabling coloring, a color selection widget will appear.
NOTE: If both cytogenetic banding and entry point coloring are enabled, the cytogenetic bands will be outlined on the entry points and filled with the specified colors. If the cytogenetic banding track has a bandType field, these band colors will be overridden by the entry point color specified.
Axis break style:
Specify the visual style to be used when indicating sequence breaks in the ideogram
Examples of the available axis break styles:
10.2.2. Entry Points List
When there is a reasonably small number of entry points available (<100), the UI will display the available entry points as a list. An entry point can be enabled/disabled for drawing by checking the Draw check-box next to the entry point name. Disabled entry points will have a gray background. By default, all *_random entry points will not be drawn.
In this selection mode, Draw All and Draw None buttons are available to quickly select all or clear all entry points for drawing, respectively.
10.2.3. Manually Specifying Entry Points
When the available entry points in a database is relatively large (>100), the UI will require the user to manually specify the entry points to be drawn by name. The UI will display the total number of entry points in the database along with a count of the current entry points specified. To add an entry point, enter the name into the text field and click the Add button. To remove an already specified entry point, select the entry point from the list and click the Remove button.
10.2.4 Individual Entry Point Properties
Entry points can have particular properties set on an individual basis. Select an entry point from the entry points list to specify these properties. The available options are described below.
Specify the label for the entry point that will appear if Draw entry point labels: is enabled.
NOTE: Circos does not handle long labels in an appropriate manner. If a label is too long, it will extend off the edge of the image. If you specify a long entry point label, a warning will appear on the Submit tab.
Individual entry point color:
If Color entry points is enabled in the Specification for All Entry Points section, then a user can specify separate colors for each entry point. This option is in the Advanced Options.
NOTE: The Color entry points option must be enabled otherwise this color will be ignored.
Entry point scaling:
Specify a global scale for the entire entry point or a local scale for portions of an entry point. The Entry Point Scales section describes this option in more detail.
Specify portions of the entry point to hide. The Entry Point Breaks section describes this option in more detail.
10.2.5 Entry Point Scales
The Entry point scaling section allows a user to specify regions of the image that should be zoomed in or out. Axis scaling is a powerful feature of Circos that gives the user power to focus a viewers attention on areas of the image that are deemed important. With scaling, you can zoom in on areas of the image that are dense with data or zoom out regions that are barren. There are two modes of axis scaling available:
10.2.6 Entry Point Breaks
The Visibility section of the interface allows a user to add axis breaks to the entry point. By adding an axis break, a user can effectively hide sections of the entry point so they are not drawn. Axis breaks can be used to hide uninteresting areas of an entry point from view. A user is required to specify the staring and ending genomic positions for the axis break (the start and end positions of the entry point to hide).
10.3 Specifying Ideogram Properties
In the Ideogram Specification section on the Specify Ideogram Details tab, a user can control some properties that affect the overall drawing of the circular image. The available options are describe below.
The chromsome units parameter defines a multiplier which can be applied to many other variable values within the configuration files. It is highly recommended to leave the value of the chromosome units as-is. However if you notice spacing issues in your image, this value can be adjusted to try to resolve those problems. This option is required.
Control the amount of whitespace between each entry point ideogram in the image. This value is required and should be specified in relation to the specified value of chromosome units. For example, if a user would like the equivalent spacing of 20 megabases between each ideogram and the chromosome units option is set to 10,000,000 (10 Mb), then a value of 2 would accomplish this. This option is required.
Specify the radius of the circular image. The radius value controls the resulting image size. This value can must be an integer greater than zero. Larger radius sizes create larger and higher resolution images, smaller radius sizes create smaller and lower resolution images.
NOTE: A user can specify any value for the radius they would like, however please note that smaller images can make it more difficult to see and comprehend dense images.
Create a microbial ideogram:
This option can be used to create the equivalent image of a microbial genome. By selecting this option, Circos will create a closed circle image resembling a traditional microbial genome image. This option is in the Advanced Options.
10.4 Tick Marks
Tick marks can provide visual cues to viewers so they can easily understand the scale and positioning of the data in your images. Tick marks can be added to the ideogram through the Tick Mark Settings section on the Specify Ideogram Details tab.
A tick mark is represented in the image as a line radiating outwards from the ideograms, spaced evenly at designated intervals. Each tick mark can also be accompanied by a tick mark label that informs viewers the spacial position of each tick. A user is required to specify the spacing of each tick mark but can also control the size of the mark and the size of the tick label. The available user options are described below.
Show tick mark:
Enable/disable the selected tick mark for drawing. This is useful to temporarily turn off a tick mark without having to delete it.
Show tick label:
Enable/disable the selected tick mark label for drawing. This is useful to temporarily turn off a tick mark without having to delete it.
Append units to the tick label:
The specified magnitude of each tick mark can be appended to the tick mark label to help a viewer better understan the genomic position of the tick mark and annotation in the image.
Tick mark spacing:
The interval to space each tick mark. This option is required.
Tick mark size:
The length (in pixels) of each tick mark that will be drawn.
Tick label size:
The font size for the accompanying tick label, if drawn.
Create grid line from tick:
Every tick mark can be specified to add a complimentary grid line. These grid lines radiate from the specified start and end positions. Grid lines can be useful for relating genomic position inside of the ideogram where annotation data will be drawn. Grid lines will be drawn on top of any highlights in the image but will be drawn underneath all other data. This option is in the Advanced Options.
An example of grid lines created from tick marks:
Grid line start:
The radial start position for the grid line created from this tick mark. Radial positions must be greater than zero. This option is in the Advanced Options.
Grid line end:
The radial end position for the grid line created from this tick mark. Radial positions must be greater than zero. This option is in the Advanced Options.
10.4.1 Adding Tick Marks
To add a tick mark, specify values for the desired options and click the Add Tick Mark button. The tick mark will be added for drawing in the ideogram.
10.4.2. Updating Tick Marks
To update the options for a tick mark, select the tick mark from the Currently Added Tick Marks List. The values for the selected tick mark will appear in the corresponding widgets. Make the desired changes and then click the Update Tick Mark button. If the button is not clicked then the changes will be lost.
10.4.3. Removing Tick Marks
To remove a tick mark from the image, select the tick mark from the Currently Added Tick Marks List. Click the Remove Tick Mark button to completely remove the tick mark.
10.5. Annotation Tracks
Any annotation track that exists in your Genboree database can be added to your Circos image and visualized in a variety of drawing types. These data plots are drawn radially outward from the center of the circle and will be drawn in the correct genomic positions. The circular composition of the data makes it extremely useful for visualizing intra- and inter-chromosomal relationships.
10.5.1 Track Types and Options
Circos supports a variety of 2D plot types that can be used to draw annotation data. In this interface, a subset of those types are supported: highlight, scatter plot, line plot, histogram, tiles, heatmaps and links. These track types are described below along with the available options.
It is important to discuss a critical option that pertains to all plot types, links and highlights. All tracks need to specify the starting and ending radial positions for where within the circular image they should be drawn. A radial position is a decimal value that is greater than zero. A radial position value between 0 - 1 will be drawn inside the circle. A radial value greater than 1 will be drawn outside the circle. Drawing annotation on both sides of the circular ideogram can produce more informative images as well as provide more drawing space to reduce clutter. Creative uses of these values can also create some visually attractive images. When adding annotation tracks, consider the value of the radial options carefully as they control the overall layout of your data.
10.5.2. Adding Annotation Tracks
To add an annotation track to the image, first select the track to add from the Available tracks list. Select the 2D plot type for the track and specify the desired options and rules. Click the Add Track button to add the annotation track. By default, the track will be drawn at the highest layer, on top of all other annotation tracks in the image, if any overlap exists.
10.5.3. Updating Annotation Tracks
To update a track, select it from the List of Currenly Added Annotation Tracks. Selecting the track item will populate the UI widgets Track Settings section with the currently set track options. Change the desired options and click the the Update Track to save the changes. If the button is not clicked then the changes will be lost.
The layering of an annotation track can be changed by selecting the track item from the list and dragging the item up or down to the desired position. Moving a track to a higher numbered layer (dragging down) will cause the track to be drawn on top of lower numbered tracks. The new layer position will automatically be saved on release.
10.5.4. Removing Annotation Tracks
To remove a track, select it from the List of Currently Added Annotation Tracks. Click the Remove Track button to completely remove the track.
10.5.5 Annotation Filtering Rules
All 2D data plots, except the histogram type, support annotation filtering rules. Here are user can add rules to filter the annotation data so that the resulting image will be affected. A condition is required, based on the annotation score, and if the condition is met, the rule will be enforced. The available properties that the rule can alter are dependent upon the type of plot selected. Rules can be useful to distinguish annotations that have differring values.
10.6 Submitting a Circos Job
When you have finished specifying how your Circos image should be created, you can submit the job to the Genboree servers for processing by going to the Submit tab.
The Submit tab also informs you of the status of you current Circos configuration. To submit a job, there must be no errors in your configuration and all of the required options must be specified. The options table at the top of the page will display the options and their current status.
The errors table will inform you of any specified options that have invalid values set. All errors must be fixed to submit a job.
The warnings table will provide information about specified options that have values that might produce unexpected results. The warnings do not have to be removed before submitting a Circos job and can be ignore if they are expected.
Upon submitting the job for processing, the server will be sent your request and return an acknowledgment. If an error occurs while communicating with the server, an error message will be returned. If the request occurs successfully, you will be informed and given a Job ID for your Circos job. When the job has finished processing, you will be notified via email and provided a link to visit so you can view the results.
If you have any questions about a submitted Circos job, contact your Genboree administrator and provide them with your Circos Job ID so they can properly assist you.