JavaScript API

class escher.Builder(map_data, model_data, embedded_css, options)

A Builder object contains all the UI and logic to generate a map builder or viewer.

Arguments:
  • map_data (object) – The data for a map, to be passed to escher.Map.from_data(). If null, then an empty Builder is initialized
  • model_data (object) – The data for a cobra model, to be passed to escher.CobraModel(). Can be null.
  • embedded_css (string) – The stylesheet for the SVG elements in the Escher map.
  • selection (object) – (Optional, Default: In the body element) The d3 selection of an element to place the Builder into. The selection cannot be inside an SVG element.
  • options (object) –
    (Optional) An object defining any of the following
    options:
    options.unique_map_id

    A unique ID that will be used to UI elements don’t interfere when multiple maps are in the same HTML document.

    options.primary_metabolite_radius

    (Default: 15) The radius of primary metabolites, in px.

    options.secondary_metabolite_radius

    (Default: 10) The radius of secondary metabolites, in px.

    options.marker_radius

    (Default: 5) The radius of marker nodes, in px.

    options.gene_font_size

    (Default: 18) The font size of the gene reaction rules, in px.

    options.hide_secondary_nodes

    (Default: false) If true, then secondary nodes and segments are hidden. This is convenient for generating simplified map figures.

    options.show_gene_reaction_rules

    (Default: false) If true, then show the gene reaction rules, even without gene data.

    options.reaction_data

    An object with reaction ids for keys and reaction data points for values.

    options.reaction_styles
    options.reaction_compare_style

    (Default: ‘diff’) How to compare to datasets. Can be either ‘fold, ‘log2_fold’, or ‘diff’.

    options.reaction_scale
    options.reaction_no_data_color
    options.reaction_no_data_size
    options.gene_data

    An object with Gene ids for keys and gene data points for values.

    options.and_method_in_gene_reaction_rule

    (Default: mean) When evaluating a gene reaction rule, use this function to evaluate AND rules. Can be ‘mean’ or ‘min’.

    options.metabolite_data

    An object with metabolite ids for keys and metabolite data points for values.

    options.metabolite_compare_style

    (Default: ‘diff’) How to compare to datasets. Can be either ‘fold’, ‘log2_fold’ or ‘diff’.

    options.metabolite_scale
    options.metabolite_no_data_color
    options.metabolite_no_data_size

    View and build options

    options.identifiers_on_map

    Either ‘bigg_id’ (default) or ‘name’.

    options.highlight_missing

    (Default: false) If true, then highlight reactions that are not in the loaded model in red.

    options.allow_building_duplicate_reactions

    (Default: true) If true, then building duplicate reactions is allowed. If false, then duplicate reactions are hidden in Add reaction mode.

    Callbacks

    options.first_load_callback

    A function to run after loading the Builder.

Callbacks

this.callback_manager.run('view_mode');
this.callback_manager.run('build_mode');
this.callback_manager.run('brush_mode');
this.callback_manager.run('zoom_mode');
this.callback_manager.run('rotate_mode');
this.callback_manager.run('text_mode');
this.callback_manager.run('load_model', null, model_data, should_update_data);
this.callback_manager.run('update_data', null, update_model, update_map, kind, should_draw);
load_map(map_data[, should_update_data])

Load a map for the loaded data. Also reloads most of the Builder content.

Arguments:
  • map_data – The data for a map.
  • should_update_data (Boolean) – (Default: true) Whether data should be applied to the map.
load_model(model_data[, should_update_data])

Load the cobra model from model data.

Arguments:
  • model_data – The data for a Cobra model. (Parsing in done by escher.CobraModel).
  • should_update_data (Boolean) – (Default: true) Whether data should be applied to the model.
view_mode()

Enter view mode.

build_mode()

Enter build mode.

brush_mode()

Enter brush mode.

zoom_mode()

Enter zoom mode.

rotate_mode()

Enter rotate mode.

text_mode()

Enter text mode.

set_reaction_data(data)
Arguments:
  • data (array) – An array of 1 or 2 objects, where each object has keys that are reaction ID’s and values that are data points (numbers).
set_metabolite_data(data)
Arguments:
  • data (array) – An array of 1 or 2 objects, where each object has keys that are metabolite ID’s and values that are data points (numbers).
set_gene_data(data)
Arguments:
  • data (array) – An array of 1 or 2 objects, where each object has keys that are gene ID’s and values that are data points (numbers).