Render information¶

SBGN says what a map means, not what it looks like. Colors, line widths and fonts are therefore not part of the SBGN-ML schema: they are stored as an extension of the map, using the vocabulary of the SBML render extension, see the SBGN-ML rendering.

libsbgnpy.render holds the python bindings of that vocabulary.

The structure¶

A RenderInformation object has three parts:

• ListOfColorDefinitions — named colors, i.e., a ColorDefinition maps an id to a hex value such as #ff9900 or #1f77b4bb with an alpha channel,
• ListOfGradientDefinitions — named gradients, i.e., a LinearGradient with its stops,
• ListOfStyles — a Style applies a G to the glyphs and arcs it lists in id_list; the G carries stroke, stroke_width, fill and the font attributes, and refers to the colors and gradients by their id.

from libsbgnpy import (
    ColorDefinition,
    G,
    ListOfColorDefinitions,
    ListOfGradientDefinitions,
    ListOfStyles,
    RenderInformation,
    Style,
)

render_info = RenderInformation(
    id="example",
    program_name="libsbgnpy",
    program_version="1.0.0",
    list_of_color_definitions=ListOfColorDefinitions(
        color_definition=[
            ColorDefinition(id="grey", value="#969696"),
            ColorDefinition(id="orange", value="#ff9900"),
        ]
    ),
    list_of_gradient_definitions=ListOfGradientDefinitions(),
    list_of_styles=ListOfStyles(
        style=[
            Style(
                id_list="glyph1 glyph2",
                g=G(stroke="grey", stroke_width=5, fill="orange"),
            ),
        ]
    ),
)

id_list is a space separated list of the ids of the glyphs and arcs the style applies to.

Storing it in a map¶

The render information is serialized and stored as an extension of the map:

from libsbgnpy import Sbgnbase, write_render_to_string

map.extension = Sbgnbase.Extension(any_element=[write_render_to_string(render_info)])

write_render_to_string writes the document without an XML declaration and without a namespace prefix, which is what belongs into an extension.

Reading it back¶

read_render_from_extension finds the renderInformation in an extension and parses it:

from pathlib import Path

from libsbgnpy import read_render_from_extension, read_sbgn_from_file

sbgn = read_sbgn_from_file(Path("map.sbgn"))
render_info = read_render_from_extension(sbgn.map[0].extension)

if render_info is not None:
    for color in render_info.list_of_color_definitions.color_definition:
        print(color.id, color.value)
        # grey #969696

It returns None if the map carries no render information. To parse a renderInformation document which is not stored in an extension use read_render_from_string.

Examples¶