This code release features improved Circlet View, now a fully interactive, exploratory tool to visualize long-range chromatin interaction data. It achieves the awesome visual effect of the "Circos plot", yet it is so much easier to work with.
You can download the source code from our server, or dropbox.
Trivia
The Circlet View function was made as part of long-range chromatin interaction visualization functionality a while ago (as seen in version 7 code release). Yet we didn't describe it on our blog then, and now that the paper is about to come out, we thought we'd better give it a formal announcement.
This function used to go under name "henge view", and one of our reviewers suggested we'd better change it... so there you go: Circlet.
Invoke Circlet View
To invoke the Circlet View, first you need to display a long-range interaction track, e.g. the following example (click here to view in browser):
Right click on the long-range track image and select "Circlet View":
The Circlet View panel will be displayed:
In this example more than one chromosomes are shown in the view (chr10, chr17, chr6, chr1). Each is identified by a blue button. The position of the button pinpoints the start of the chromosome, which means the clockwise direction is 5' to 3' on chromosome sequence.
Rearrange chromosomes
To move chr10 to overpass chr17 in this example, press on chr10 button and drag down, orange arc highlights the suggested position of chr10:
After moving sufficient distance, chr10 will swap its position with chr17:
Zoom in & out
By default the whole chromosome is shown. You can zoom in and show only a sub section by dragging on chromosome bar:
Following shows updated graph with partially shown chr10 (the region where all arcs originates from):
To zoom out, right click on chr10 name button and press "Zoom out" option:
Configure rendering style
Right click on white space of the graph to invoke the configuration panel:
By right clicking on chromosome bar, you will see a list of chromosomes used in the view. This is primarily for adding a chromosome back after you got it removed.
Add "wreath tracks"
At the top of the graph click , a list of currently displayed tracks in the browser is shown:
Here I click tracks "RefSeq genes" and "GC percent" to add them to my current view:
The gene track is displayed as density (green), and GC percent track is in blue.
To configure a track, right click on a track to get the options:
We love this function and hope you can find it useful. We will continue to work and improve it:
You can download the source code from our server, or dropbox.
Trivia
The Circlet View function was made as part of long-range chromatin interaction visualization functionality a while ago (as seen in version 7 code release). Yet we didn't describe it on our blog then, and now that the paper is about to come out, we thought we'd better give it a formal announcement.
This function used to go under name "henge view", and one of our reviewers suggested we'd better change it... so there you go: Circlet.
Invoke Circlet View
To invoke the Circlet View, first you need to display a long-range interaction track, e.g. the following example (click here to view in browser):
Right click on the long-range track image and select "Circlet View":
The Circlet View panel will be displayed:
In this example more than one chromosomes are shown in the view (chr10, chr17, chr6, chr1). Each is identified by a blue button. The position of the button pinpoints the start of the chromosome, which means the clockwise direction is 5' to 3' on chromosome sequence.
Rearrange chromosomes
To move chr10 to overpass chr17 in this example, press on chr10 button and drag down, orange arc highlights the suggested position of chr10:
After moving sufficient distance, chr10 will swap its position with chr17:
Zoom in & out
By default the whole chromosome is shown. You can zoom in and show only a sub section by dragging on chromosome bar:
Following shows updated graph with partially shown chr10 (the region where all arcs originates from):
To zoom out, right click on chr10 name button and press "Zoom out" option:
Configure rendering style
Right click on white space of the graph to invoke the configuration panel:
By right clicking on chromosome bar, you will see a list of chromosomes used in the view. This is primarily for adding a chromosome back after you got it removed.
Add "wreath tracks"
At the top of the graph click , a list of currently displayed tracks in the browser is shown:
Here I click tracks "RefSeq genes" and "GC percent" to add them to my current view:
The gene track is displayed as density (green), and GC percent track is in blue.
To configure a track, right click on a track to get the options:
We love this function and hope you can find it useful. We will continue to work and improve it:
- Remedy the limit of showing regional data only. We will allow you to display Hi-C data on full chromosomes, or even the whole genome, as easy as above steps.
- You will be able to overlay two tracks inside the same plot and show them as separate colors to compare.
- SVG output.
- Make it a plug-in web app. Think about displaying an interactive Circlet plot in your webpage, isn't that cool?
