lib5c.plotters.extendable package

Submodules

• lib5c.plotters.extendable.base_extendable_heatmap module
• lib5c.plotters.extendable.bed_extendable_heatmap module
• lib5c.plotters.extendable.chipseq_extendable_heatmap module
• lib5c.plotters.extendable.cluster_extendable_heatmap module
• lib5c.plotters.extendable.domain_extendable_heatmap module
• lib5c.plotters.extendable.extendable_figure module
• lib5c.plotters.extendable.extendable_heatmap module
• lib5c.plotters.extendable.gene_extendable_heatmap module
• lib5c.plotters.extendable.legend_extendable_heatmap module
• lib5c.plotters.extendable.motif_extendable_heatmap module
• lib5c.plotters.extendable.rectangle_extendable_heatmap module
• lib5c.plotters.extendable.ruler_extendable_heatmap module
• lib5c.plotters.extendable.snp_extendable_heatmap module

Module contents

Module describing the extendable heatmap plotting system.

The core idea behind this system is the ExtendableFigure API. Subclasses of ExtendableFigure inherit the add_ax() instance method, which tacks on additional matplotlib axes to an existing axis using a divider object obtained using the matplotlib function mpl_toolkits.axes_grid1.make_axes_locatable(). The new axes are stored in an axes dict instance variable on the ExtendableFigure and can subsequently be plotted on with any matplotlib-based function.

This means that an arbitrary number of additional data tracks can be added to the ExtendableFigure in a sequential, interactive manner.

The BaseExtendableHeatmap class extends ExtendableFigure and implements extra functionality specific for plotting contact frequency heatmaps. This includes a custom interface to add_ax() called add_margin_ax(), designed to make it easy to add tracks to the margins of a contact frequency heatmap.

In order to handle the wide diversity of tracks and overlays that may be added to a contact frequency heatmap, a wide variety of plug-in mixin classes are defined. These mixin classes each implement one specific feature in the form of a few related instance methods that internally call add_margin_ax(). For example, ChipSeqExtendableHeatmap provides a function add_chipseq_track() which uses add_margin_ax() to add a ChIP-seq track to the ExtendableHeatmap. The separation of different features into separate mixin classes makes the code easier to understand and also makes it easy to add new features.

The feature functions like add_chipseq_track() typically accept some data as well as parameters for creating the new axis. The functions typically create the new axis using add_margin_ax(), passing through the relevant parameters. The functions then plot the data to the newly created axis using matplotlib plotting functions. Finally, they return the new axis.

By convention, we often plot tracks on both the left and the bottom of the heatmap. To make this easier, most feature functions like add_chipseq_track() have associated helper functions like add_chipseq_tracks(), which simply calls add_chipseq_track() twice: once with loc='bottom' and once with loc='left'.

To add a new feature:

1. create a new mixin class extending BaseExtendableHeatmap that implements the functions for your feature,

2. place your new class in the lib5c.plotters.extendable module,

3. import your class in the top level module file __init__.py and add it to the __all__ variable, and

4. add your class to the list of classes inherited by ExtendableHeatmap, making sure to place it before BaseExtendableHeatmap in the list.

In the future, this process may be automated.