lib5c.plotters.extendable.domain_extendable_heatmap module

Module for the DomainExtendableHeatmap class, which adds domain outlining functionality for the extendable heatmap system.

class lib5c.plotters.extendable.domain_extendable_heatmap.DomainExtendableHeatmap(array, grange_x, grange_y=None, colorscale=None, colormap='obs', norm=None)

Bases: lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap

ExtendableHeatmap mixin class providing ChIP-seq domain outlining functionality.

outline_domain(domain, color='green', linewidth=2, upper=True)

Outlines a contact domain on the heatmap.

Parameters

• domain (dict) –

  A genomic feature dict describing the domain to be outlinerd. Should be a dict with at least the following keys:

  {
      'chrom': str,
      'start': int,
      'end': int
  }
  

  ’start’ and ‘end’ should be in units of base pairs (this function will handle the conversion to heatmap pixel units).

• color (matplotlib color) – The color to outline the domain with.

• linewidth (float) – The line width to use when outlining the domain. Pass a larger number for a thicker, more visible outline.

• upper (bool) – Pass True to draw the outline in the upper triangle of the heatmap. Pass False to draw it in the lower triangle.

outline_domains(domains, color='green', linewidth=2, upper=True)

Outlines a set of contact domains on the heatmap by repeatedly calling outline_domain().

Parameters

• domains (list of dict) –

  A list of domains, where each domain is represented as genomic feature dict with at least the following keys:

  {
      'chrom': str,
      'start': int,
      'end': int
  }
  

  ’start’ and ‘end’ should be in units of base pairs (this function will handle the conversion to heatmap pixel units).

• color (matplotlib color) – The color to outline the domains with.

• linewidth (float) – The line width to use when outlining the domains. Pass a larger number for a thicker, more visible outline.

• upper (bool) – Pass True to draw the outlines in the upper triangle of the heatmap. Pass False to draw them in the lower triangle.