cobramod.core.pathway ===================== .. py:module:: cobramod.core.pathway .. autoapi-nested-parse:: COBRApy Group-child class extension The new class :class:`cobramod.pathway.Pathway` is child derived from :class:`cobra.core.group.Group`. It extends some functionalities such as: - solution: Obtain the solution for the specific members. - visualize: get a :class:`escher.Builder` for that specific Pathway. Attributes ---------- .. autoapisummary:: cobramod.core.pathway.debug_log Exceptions ---------- .. autoapisummary:: cobramod.core.pathway.GraphKeyError Classes ------- .. autoapisummary:: cobramod.core.pathway.EscherIntegration cobramod.core.pathway.ForceGraphIntegration cobramod.core.pathway.JsonDictionary cobramod.core.pathway.Pathway Functions --------- .. autoapisummary:: cobramod.core.pathway.model_convert Module Contents --------------- .. py:class:: EscherIntegration(map_name = None, map_json = None, reaction_data = None, reaction_scale = None, reaction_styles = None, never_ask_before_quit = False) Bases: :py:obj:`anywidget.AnyWidget` .. versionadded:: 1.3.0 An alternative Python integration for `Escher `_ . .. py:attribute:: reaction_styles :type: Optional[List[Any]] .. py:attribute:: map_name .. py:attribute:: map_json .. py:attribute:: reaction_scale .. py:attribute:: reaction_data :type: Optional[Dict[str, float]] .. py:attribute:: never_ask_before_quit .. py:property:: model_data .. py:property:: embedded_css .. py:property:: options .. py:method:: save_html(filepath) This method creates a standalone HTML file that contains all the data of the Escher map and loads it automatically when it is opened. :param filepath: The file in which the HTML file is to be saved. .. py:class:: ForceGraphIntegration Bases: :py:obj:`anywidget.AnyWidget` .. versionadded:: 1.3.0 Widget for displaying a :py:class:`cobra.core.group.Group` or :py:class:`cobra.Reaction` as a force directed graph. .. py:property:: model :type: Optional[Union[Type[cobra.core.Group], Type[cobra.Reaction]]] The Model to be represented. It can ether be a :py:class:`cobra.core.group.Group` or :py:class:`cobra.Reaction`. It is set to None upon initialization. .. py:property:: solution :type: Optional[Union[Type[cobra.Solution], dict[str, float]]] The flux values to be taken into account when creating the graph. These scale the stoichiometry of the respective reaction. If a reaction is not found in this object, a flux of 1 is assumed. The flux values can either be passed as cobra.Solution or as dict, where the key is the reaction ID and the value is the flux value. It is set to None upon initialization. .. py:method:: save_layout(file) Method to save the layout of the current display. The resulting file is a CSV containing the ID of the metabolite and its X, Y and Z position in the other columns. :param file: The path where the layout is to be saved. .. py:method:: load_layout(file) Method to restore the layout that was saved using :py:meth:`~cobramod.visualization.force_graph.ForceGraphIntegration.save_layout`. :param file: Path to the file containing the saved layout. .. py:data:: debug_log .. py:exception:: GraphKeyError Bases: :py:obj:`Exception` Simple Error that should be raised when a value is missing as key in a graph .. py:class:: JsonDictionary Bases: :py:obj:`collections.UserDict` Create a JsonDictionary object which can be used to parse information into JSON files to be later read by Escher. When creating the object, some keyword arguments may be passed. :keyword head: General information of the JSON. Keys included: map_name, map_id, map_description, homepage, schema. :kwtype head: dict, optional :keyword reactions: Dictionary with multiple :class:`cobramod.visualization.items.Reaction` where the key is the number of the reaction and the value the object. Defaults to empty dictionary. :kwtype reactions: dict, optional :keyword nodes: Dictionary with multiple :class:`cobramod.visualization.items.Node` where the key is the number of the Node and the value the corresponding object. Defaults to empty dictionary. :kwtype nodes: PairDictionary :keyword text_labels: Dictionary with the custom text inside the canvas. :kwtype text_labels: dict, optional :keyword canvas: x and y position, width and height of the white area in Escher. :kwtype canvas: dict, optional .. attribute:: CANVAS_WIDTH Width for the canvas. Defaults to 1500. :type: float .. attribute:: CANVAS_HEIGHT Height for the canvas. Defaults to 1500. :type: float .. attribute:: R_WIDTH Width of a reaction. Defaults to 350. :type: float .. attribute:: R_HEIGHT Height of a reaction. Defaults to 270. :type: float .. attribute:: reaction_data Dictionary with the solution to be visualized. Default to empty dictionary. :type: Dict[str, float] .. py:method:: get_canvas() .. py:method:: json_dump(indent = None) Returns a string that is the JSON representation of this class. :param indent: Defines the indentation for the JSON. Defaults to None. :type indent: int .. py:method:: add_metabolite(x, y, label_x, label_y, bigg_id, name, node_is_primary) Add a metabolite-type node into the JsonDictionary. The key will be always the last node number. :param x: Position in x-axis for the node. :type x: float :param y: Position in y-axis fot the node. :type y: float :param label_x: Position of the label in the x-axis. :type label_x: float :param label_y: Position of the label in the y-axis. :type label_y: float :param bigg_id: Identifier of the metabolite. It does not have to be from BIGG. :type bigg_id: str :param name: Name of the label for the metabolite. :type name: str :param node_is_primary: True if node should represent a primary metabolite, i.e. Node is visually larger. :type node_is_primary: bool .. py:method:: add_marker(x, y, node_type) Add a marker-type node into the JsonDictionary. Node can be a midmarker or a multimarker. These markers are located in the middle of the reaction. A midmarker is located between two multimarkers. :param x: Position in x-axis for the node. :type x: float :param y: Position in y-axis for the node. :type y: float :param node_type: Type of marker. Options: 'midmarker' or 'multimarker'. :type node_type: str .. py:method:: map_metabolites(metabolite_dict, reaction, top_edge, left_edge, vertical) Creates the metabolites from given dictionary and complements the :class:`cobramod.visualization.items.Reaction`. Moreover, it creates the corresponding metabolites-nodes for the JsonDictionary class. :param metabolite_dict: Dictionary with metabolites and their coefficients. :type metabolite_dict: dict :param reaction: Reaction that will include the metabolite. :type reaction: Reaction :param top_edge: Position for the top edge of the reaction-box. :type top_edge: float :param left_edge: Position for the left edge of the reaction-box. :type left_edge: float :param vertical: Defines if metabolite should be map vertically. :type vertical: bool .. py:method:: add_segments(reaction, metabolite_dict) Add the segments to given Reaction. This will make the visuals in Escher. The information about the nodes of metabolites in located in the JsonDictionary. A reaction will have 2 + number of metabolite as its number of segments. :param metabolite_dict: Dictionary with metabolites and their coefficients. :type metabolite_dict: dict :param reaction: Reaction to extend. :type reaction: Reaction .. py:method:: add_reaction(row, column, string, name, identifier, vertical) Parses and add given reaction string as a reaction for the JsonDictionary. It will automatically create all the necessary nodes and segments for the JSON. :param string: Reaction string to be parsed. :type string: str :param identifier: Identifier for the reaction. :type identifier: str :param row: Row number from the visualization matrix. :type row: int :param column: Column number of the visualization matrix. :type column: int :param name: The name of the reaction. :type name: str :param vertical: If reaction should be displayed vertically. :type vertical: bool .. py:method:: color_grading(color, min_max = None, quantile = False, max_steps = 100, n_steps = None) Function that creates a color scale between two predefined colors. The number of color gradations corresponds to the number of fluxes. :param color: list of two colors. The first color defines the endpoint for positive values, the second for negative values. The colors must be passed in their rgb representation. :type color: list of str or list of list of int :param min_max: List consisting of two floats. The first int describes the minimum, the second the maximum. These two values are additionally added as data values and at the same time ensure that all values greater or less than these are ignored when creating the gradient. :type min_max: list of float,optional :param quantile: Defines whether quantiles are to be used for the creation of the gradient. Otherwise, the steps are equally distributed between the minimum and maximum. :type quantile: bool, optional :param n_steps: Sets the number of color steps. :type n_steps: int, optional :param max_steps: Sets the maximum number of color steps. :type max_steps: int, optional .. py:method:: visualize(filepath, vertical = False, color = None, min_max = None, quantile = False, max_steps = 100, n_steps = None, custom_integration = False, never_ask_before_quit = False) Saves the visualization of the JsonDictionary in given path as a HTML. Returns the builder for the JsonDictionary. If method is called in Jupyter or Qtconsole, it will show the embedded builder of the escher visualization. Else, it will open the default browser of the operating system and will load the previously saved HTML. .. note:: Blank spaces are removed from the reactions. :param filepath: Path, optional Path for the HTML. Defaults to "pathway.html" in the current working directory :param vertical: bool, optional Defines if pathway should be illustrated vertically. Defaults to False. :param color: list of str or list of lost of int, optional A list consisting of two entries. These define the endpoints for a color gradient. The entries can either be the colors as a list with three elements that define the RGB values or a string that defines the color name according to the css standard. If None is used here, no gradient will be generated. Defaults to None. Example: ["orange", "green"] or [[255, 165, 0], [0, 128, 0]] :param min_max: list of float, optional List consisting of two ints. The first int describes the minimum, the second the maximum. These two values are additionally added as data values and at the same time ensure that all values greater or less than these are ignored when creating the gradient. With Quantile = False, a data-independent gradient is created. :param quantile: bool, optional Defines whether quantiles are to be used for the creation of the gradient. Otherwise, the steps are equally distributed between the minimum and maximum. :param max_steps: int, optional Sets the maximum number of color steps. :param n_steps: int, optional Sets the maximum number of color steps. :returns: Escher builder object for the visualization :rtype: Builder .. seealso:: Color names according to the css standard: https://www.w3schools.com/cssref/css_colors.asp .. py:class:: Pathway(id, name = '', members = None, kind = None) Bases: :py:obj:`cobra.core.Group` A Sub-class from the original COBRApy :class:`cobra.Group`, which inherits all attributes and adds the method solution, to get a Solution for the members of this Class. Attributes vertical (bool, optional): Variable that determines whether the display should be vertical or horizontal using Escher. Defaults to False. color_negative (str or list of int, optional) : The color to use as the endpoint for the negative fluxes during the creation of the color gradient. All colors of the CSS standard can be used here or their RGB representation. color_positive (str or list of int, optional) : The color to use as the endpoint for the positive fluxes during the creation of the color gradient. All colors of the CSS standard can be used here or their RGB representation. color_min_max (list of float, optional) : The maximum and minimum to be taken into account when creating the color gradient. This creates these two values artificially to allow the creation of a data-independent color gradient. Fluxes larger or smaller are ignored accordingly. color_quantile (bool, optional) : Attribute that defines whether the color gradient should be determined through quantiles or equally distributed between the maximum and the minimum. Defaults to False which means that the gradations are evenly distributed. color_n_steps (int, optional) : The number of steps used when creating the color gradient. Uses the number of fluxes by default. The default value is None. color_max_steps (int, optional) : The maximum number of steps to use when creating the color gradient. Default value is 100. .. seealso:: Color names according to the css standard: https://www.w3schools.com/cssref/css_colors.asp .. py:method:: add_members(new_members) Add given list of :class:`cobra.core.reaction.Reaction` into the Pathway. :param new_members: List of Reactions to add to the class. :type new_members: list :raises TypeError: If not all members are proper Reaction objects. .. py:method:: solution(solution) Returns a :class:`cobra.Solution` with only the members of the pathway. :param solution: Original COBRApy :class:`cobra.Solution` to filter. :type solution: Solution :returns: Filtered solution containing only members of the Pathway class. :rtype: Solution .. py:method:: modify_graph(reaction, next_reaction) Modifies the order of the graph. This is useful when merging multiple pathways or joining reactions. In the graph, the selected reaction will be forced to show "next_reaction" as its successor. :param reaction: Identifier of the reaction to modify in the graph. :type reaction: str :param next_reaction: Identifier of the next reaction. This reaction will take place after "reaction". If None is passed, then "reaction" will not have successors. :type next_reaction: str, None :raises GraphKeyError: If the reaction or the next_reaction does not appear :raises in the graph of the pathway.: .. py:method:: visualize(solution_fluxes = None, filename = None, vis = 'escher', never_ask_before_quit = False) .. versionchanged:: 1.3.0 The 'vis' parameter has been added. This allows one to choose between different visualization tools. Returns a :class:`escher.Builder`, which can be used to create visual representations of the pathway. :param solution_fluxes: Series or Dictionary with fluxes. The values will be then showed in the Builder. Defaults to None. :param filename: Path for the HTML. Defaults to "pathway.html" in the current working directory. :param vis: .. versionadded:: 1.3.0 Parameter that determines the visualization tool used. It is possible to choose between the original Escher integration [escher], the one embedded in CobraMod [escher-custom] and a 3-dimensional force directed graph visualization [3d-force]. .. deprecated:: 1.3.0 The original python integration of Escher will be removed in a future version due to dependency conflicts with Jupyter. The integration embedded in CobraMod will take its place in the future. This can already be used by setting 'vis' to "escher-custom". :param never_ask_before_quit: .. versionadded:: 1.3.0 Option to control whether a warning dialog is displayed when the Escher Builder window is closed. Only has an effect when using Escher for visualization. .. py:function:: model_convert(model) Converts all Group objects in the given model to proper cobramod :class:`cobramod.pathway.Pathway`