Contact map style configuration - ma-compbio/Higashi GitHub Wiki

In this documentation, all panels would be marked with Bold Italic, any components (buttons, sliders, menus) in the tool would be marked with code format. Similar to before, the file names are also marked with code format.

Configure the styles of the contact maps

Color map and value range of the contact maps

Since the raw contact maps and imputed contact maps from different methods have different value scales, in Higashi-vis, we define the Vmin/Vmax based on the quantile. Specifically, when the Vmin/Vmax(% of range) is defined as x, Vmin = [(1-x)/2]*100 th quantile of the values, Vmax = [(1+x)/2]*100 th quantile of the values.

In Higashi-vis, we provided several common color maps including Reds, RdBu, viridis, and cmo.curl (the one used in Higashi manuscript). cmo.curl requires the package cmocean to be installed. Specifically, Reds and viridis work better on raw contact maps while RdBu, cmo.curl work better on imputed ones.

Normalization of the contact maps

In Higashi-vis, we provide several normalization methods or processing methods on the contact maps including VC_SQRT (VC_SQRT), Quantile Transformation (Quantile_norm), and Pearson correlation on the O/E matrix (Compartment). See below for examples:

Inspect a part of the contact maps

In Higashi, we provided several methods for the fast location of a part of the contact maps.

The same as the Embedding visualization panel, the Contact map visualization panel supports drag and zoom-in/out with mouse as well.

If the user has a specific region in mind, the Heatmap start x, Heatmap end x, Heatmap start y, Heatmap end y sliders serve as the "go to" function as the commonly used genome browser. The unit here is the number of bins. So the user needs to turn the genome coordinate into the index of the bins before using the sliders.

To focus on the near-diagonal part of the contact maps, the user can use the Heatmap distance slider to choose the maximum genomic distance of the contact maps to visualize. Same as above, the unit is the number of bins.

One can also rotate the contact maps by 45 degrees to inspect the TAD-like domain structures.