synthaser.plot

This modules handles the construction of synthaser visualisations.

synthaser plots are implemented as HTML documents with embedded visualisations created using the D3 JavaScript library. Files used in this process are all stored separately inside the plot folder in the source code (i.e. separate CSS, JavaScript, HTML).

This module provides two ways to construct a synthaser plot from a collection of Synthase objects: hosting using Python’s built in socketserver module, or generating a completely static HTML file containing all code elements necessary for the plot.

1. Get necessary data

>>> data = plot.get_data(synthases)

This generates a dictionary which can be converted easily to JSON and given to the JavaScript visualisation. It contains a dictionary of the Synthase objects, the order in which they should be drawn, a dictionary of Synthase objects grouped by their classifications, and the annotation group hierarchy generated using grouping.get_annotation_groups().

2. 1. Dynamically serve plots using socketserver

>>> plot.serve_html(data)

This will host the visualisation on some randomly chosen open port on localhost. It requires a keyboard interrupt to stop serving the plot.

2. 2. Generate static HTML file

>>> plot.save_html(data, "myoutput.html")

This will generate a completely static HTML file containing all code elements required to render the plot (JavaScript and CSS embedded directly in the HTML file). This can then be moved/copied anywhere you would like.

This workflow is mirrored by the plot_synthases function:

>>> plot.plot_synthases(synthases, output="myoutput.html")

class synthaser.plot.CustomHandler(data, *args, **kwargs)

Handler for serving cblaster plots.

do_GET()

Serves each component of the cblaster plot.

log_message(format, *args)

Suppresses logging messages on every request.

synthaser.plot.plot_synthases(container, output=None)

Generates synthaser plot from a collection of Synthase objects.

synthaser.plot.save_html(data, output)

Generates a static HTML file with all visualisation code.

synthaser.plot.serve_html(data)

Serve a synthaser plot using the socketserver module.