10. Python API¶
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class
escher.Builder(map_name: str = None, map_json: str = None, model: cobra.core.model.Model = None, model_name: str = None, model_json: str = None, **kwargs)¶ A Python wrapper for the Escher metabolic map.
This map will also show data on reactions, metabolites, or genes.
The Builder is a Jupyter widget that can be viewed in a Jupyter notebook or in Jupyter Lab. It can also be used to create a standalone HTML file for the map with the save_html() function.
Maps are downloaded from the Escher website if found by name.
- Parameters
height (int) – The height of the Escher Jupyter widget in pixels.
map_name (str) – A string specifying a map to be downloaded from the Escher website.
map_json (str) – A JSON string, or a file path to a JSON file, or a URL specifying a JSON file to be downloaded.
model – A COBRApy model.
model_name – A string specifying a model to be downloaded from the Escher web server.
model_json – A JSON string, or a file path to a JSON file, or a URL specifying a JSON file to be downloaded.
embedded_css –
The CSS (as a string) to be embedded with the Escher SVG. In Jupyter, if you change embedded_css on an existing builder instance, the Builder must be restarted for this to take effect (e.g. by re-evaluating the widget in a cell). You can use the default embedded css as a starting point:
https://github.com/zakandrewking/escher/blob/master/src/Builder-embed.css
reaction_data – A dictionary with keys that correspond to reaction IDs and values that will be mapped to reaction arrows and labels.
metabolite_data – A dictionary with keys that correspond to metabolite IDs and values that will be mapped to metabolite nodes and labels.
gene_data – A dictionary with keys that correspond to gene IDs and values that will be mapped to corresponding reactions.
Keyword Arguments
You can also pass in any of the following options as keyword arguments. The details on each of these are provided in the JavaScript API documentation:
use_3d_transform
menu
scroll_behavior
use_3d_transform
enable_editing
enable_keys
enable_search
zoom_to_element
full_screen_button
disabled_buttons
semantic_zoom
starting_reaction
never_ask_before_quit
primary_metabolite_radius
secondary_metabolite_radius
marker_radius
gene_font_size
hide_secondary_metabolites
show_gene_reaction_rules
hide_all_labels
canvas_size_and_loc
reaction_data
reaction_styles
reaction_compare_style
reaction_scale
reaction_no_data_color
reaction_no_data_size
gene_data
and_method_in_gene_reaction_rule
metabolite_data
metabolite_styles
metabolite_compare_style
metabolite_scale
metabolite_no_data_color
metabolite_no_data_size
identifiers_on_map
highlight_missing
allow_building_duplicate_reactions
cofactors
enable_tooltips
enable_keys_with_tooltip
reaction_scale_preset
metabolite_scale_preset
primary_metabolite_radius
secondary_metabolite_radius
marker_radius
gene_font_size
reaction_no_data_size
metabolite_no_data_size
If any of these is set to None, the default (or most-recent) value is used. To turn off a setting, use False instead.
All arguments can also be set by assigning the property of an an existing Builder object, e.g.:
my_builder.map_name = 'iJO1366.Central metabolism'
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display_in_browser(*args, **kwargs)¶ Deprecated.
We recommend using the Jupyter Widget (which now supports all Escher features) or the save_html option to generate a standalone HTML file that loads the map.
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display_in_notebook(*args, **kwargs)¶ Deprecated.
The Builder is now a Jupyter Widget, so you can return the Builder object from a cell to display it, or you can manually call the IPython display function:
from IPython.display import display from escher import Builder b = Builder(…) display(b)
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save_html(filepath)¶ Save an HTML file containing the map.
- Parameters
filepath (string) – The name of the HTML file.