The HiC Heatmap Plot

The HiC heatmap plot is a global way of being able to look at the strengths of interaction between different regions of the genome. It is only available when the currently active DataStore is a HiC dataset.

You access this plot by selecting "Plots > HiC heatmap" you can then choose whether the axes for the plot are shown as genomic coordinates, or as sets of probe lists which you can then select.

The plot shows two copies of the genome at right angles to each other and between these it draws a heatmap showing the density of paired reads which fall into each interacting pair of regions in the plot. The potentially interacting regions are taken from the currently active probe list.

A Line Graph

To zoom into the plot you can simply drag a box within the main plot area. To zoom out press the right mouse button. If you hold the control key while zooming out only the x axis will zoom out. If you hold down shift then only the y-axis will zoom out.

If you double click on any interaction point then one end of the interaction will be shown in the main chromosome view. If you shift+double click then the other end will be shown.

Options

There are a number of different filtering options which apply to this plot. You can apply most of the filters either before the plot is calculated or after it has been displayed. The filters you apply before calculating the plot are hard limits which allow the program to immediately discard many of the potential interactions to leave a manageable subset of interactions to display. Many of the same options appear after the plot has been drawn and these can be changed interactively, but at this stage the filters can only be set to values more restrictive than those initially chosen when the plot what calculated.

Pre-calculation options

HiC pre-calculation options

Post-calculation options

Once the plot has been drawn you can adjust all of the values set in the pre-calculation filters. In addition you have some more options.