cameo.visualization package

Submodules

cameo.visualization.escher_ext module

class cameo.visualization.escher_ext.NotebookBuilder(*args, **kwargs)

Bases: escher.plots.Builder

Methods

display_in_browser([ip, port, n_retries, …])	Launch a web browser to view the map.
display_in_notebook([js_source, menu, …])	Embed the Map within the current IPython Notebook.
save_html([filepath, overwrite, js_source, …])	Save an HTML file containing the map.

update

update(reaction_data=None, metabolite_data=None, gene_data=None, reaction_scale=None)

cameo.visualization.palette module

class cameo.visualization.palette.PaletteMapper

Bases: object

Methods

add_palettalbe_palette
map_palette

add_palettalbe_palette(name, palette)

map_palette(name, n=3, reverse=False)

cameo.visualization.sympy_ext module

cameo.visualization.visualization module

cameo.visualization.visualization.draw_knockout_result(model, map_name, simulation_method, knockouts, *args, **kwargs)

cameo.visualization.visualization.inchi_to_svg(inchi, file=None, debug=False, three_d=False)

Generate an SVG drawing from an InChI string.

Parameters:

inchi : str

An InChI string.

Returns:

str

A vector graphics of the compound represented as SVG.

<svg version=”1.1” id=”topsvg” xmlns=”http://www.w3.org/2000/svg” xmlns:xlink=”http://www.w3.org/1999/xlink” xmlns:cml=”http://www.xml-cml.org/schema” x=”0” y=”0” width=”200px” height=”200px” viewBox=”0 0 100 100”> <title>OBDepict</title> <rect x=”0” y=”0” width=”100” height=”100” fill=”white”/> <text text-anchor=”middle” font-size=”6” fill =”black” font-family=”sans-serif” x=”50” y=”98” ></text> <g transform=”translate(0,0)”> <svg width=”100” height=”100” x=”0” y=”0” viewBox=”0 0 80 80” font-family=”sans-serif” stroke=”rgb(0,0,0)” stroke-width=”2” stroke-linecap=”round”> <text x=”36” y=”48” fill=”rgb(255,12,12)” stroke=”rgb(255,12,12)” stroke-width=”1” font-size=”16” >OH</text> <text x=”60” y=”51.68” fill=”rgb(255,12,12)” stroke=”rgb(255,12,12)” stroke-width=”1” font-size=”13” >2</text> </svg> </g> </svg>

‘ # noqa

cameo.visualization.visualization.graph_to_svg(g, layout=<function fruchterman_reingold_layout>)

return the SVG of a matplotlib figure generated from a graph

Module contents