Options ¬
You may customize the charts in the parent Reaction Traffic node with the many options available in this node. You may view just the reaction network, or choose to add the traffic amounts in each pathway of the network. Traffic charts are done by displaying the width of the arrows in proportion to the relative transit of selected variable along the reaction network. You may highlight or isolate pathways for certain compounds of interest. You may also configure colors, shapes, the ranking order of appearance, and create subgraphs. Each of these options is explained in detail below.

Tabbed Views



Tabbed Views

General

Compounds

Reactions



General

This view provides the main set of configuration options for the graph. It has three grids, which are explained below:


Grid Views

Graph Options

Pathways

SubGraphs


Graph Options

The options available are described below:

  • Graph Direction
    It allows you to set the direction of the graph. By default, the graph is laid out from Top -> Bottom. Other options available are Left -> Right, Bottom -> Top and Right -> Left.

  • Merge Lines
    This allows for partially parallel arrows to share part of their path, thus reducing clutter. However, it is not recomended to enable this option when Display Pathway Traffic for Variable is enabled.

  • Green-Fill Measured Species
    This option only appears when Estimation is the Selected Mode for the active project, and is used to identify compounds with measurements.
    The compounds that have at least one non-zero measurement in the included experimental sets are filled in green. If this option is selected, you will not be able to change the colors or shape of these compounds in the Compounds tab.

  • Highlight Pathway
    This option allows you to highlight or isolate the reaction pathways for specific compounds of interest. To use this feature, select the compounds of interest in the Pathways grid. By default, this option is enabled.

  • Show Compounds by:
    In the combo, you may choose to label the compound nodes by the Name or Formula of the compound. The compound Name is used by default.

  • Show Reactions by:
    In the combo, you may choose to label the reaction nodes by the Name or Equation of the reaction. The reaction Name is used by default.

  • Display Pathway Traffic for Variable
    By enabling this option, you can visualize the magnitude of Moles, Mass or Atoms traffic in the paths of the reaction network.
    Each path of the network is displayed with an arrow whose width is proportional to the amount of traffic for the selected variable. The traffic is calculated as the total quantity(not rate) of moles, mass or atoms that have traveled the pathway. These are calculated for each experimental set (or optimization case). The traffic values are then averaged among all sets included in Experiments node if working in Mode Estimation, or among included cases in Case Design node if the project is in Mode Optimization.
    The following combos are shown when this option is enabled:
      • Variable
        You may select the variable for which the traffic is to be drawn.
        The default option is Moles. The other options are Atom moles and Compound Mass. Only the atoms that are present are shown. In other words, only atoms that have non-zero values in the Formula node are shown. Similarly, Mass is shown only if there is at least one non-zero atom value in the Formula node. Molecular weights are calculated automatically based on the atom counts loaded in the Formula node. The user provided Molecular weights are not used.
      • Directions Shown
        By selecting Both, the traffic arrows are shown for each reaction direction. When choosing Net, only the direction that has higher traffic is displayed in the chart, and its width is proportional to the net traffic on the reaction.
      • Max Arrow Width
        This value represents the maximum arrow width to be drawn.
        The pathway with the highest traffic is displayed with its width as selected here. Other paths will have a smaller width, in proportion to their traffic compared to the highest traffic in the network.
          Note1: If you hide some compounds or reactions in the Compounds and/or Reactions tabs, then this maximum width is assigned to the path with the highest traffic among the non-hidden pathways. In general, if you hide the compound and/or reaction node related to the highest traffic, the following busiest path will be drawn with the maximum width chosen here. In order to estimate the magnitude of the reduction of the traffic, we display the ratio of the maximum traffic among all reactions and the maximum traffic in the current display. This information is displayed at the bottom of the picture in the Reaction Traffic node.
          Note2: Since the quasi-equilibrium assumption implies very high rates, the rate arrows for equilibrated reactions are shown with maximum width when the Both option is selected in Directions Shown option.
      • Min Arrow Width
        This value represents the minimum width for the traffic arrows. Arrows for reactions with very low traffic whose width would be smaller that the minimum selected, are shown or hidden depending on your choice in the following option.
      • Traffic Display Range Message
        There is a linear mapping between the arrow width and traffic values. In REX, the traffic values are normalized with respect to the maximum traffic. Thus, the traffic values range from 100%(Max Traffic) to values that could be as low as zero. The arrows however span only a finite range, between the Max Arrow Width and the Min Arrow Width. Thus, the total traffic range that can be displayed is between 100%(=Max Traffic) to (100/MaxArrowWidth)*(MinArrowWidth) %, which we call the threshold. For reaction traffic values that fall below this threshold, you may decide whether to hide or show them as described in the next option.
      • If Traffic less than threshold
        By selecting the default option, Use Min Width, these traffic arrows are displayed with the minimum width.
        The option Lighten arrows draws these paths with a lighter gray color. Thus, the image appears less crowded while keeping the node positions same as with the previous option.
        The option Remove arrows hides all these low traffic paths.

  • Show Image button
    Clicking this button will take you directly to the parent Reaction Traffic node.

  • Export Image button
    On clicking this, you may save the network image as a .png file.

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Pathways

In this grid, you may select the compounds whose pathways are to be highlighted.
By default, no compound is selected, thus the reaction network does not highlight the pathway of any compound in particular.

The Pathway Display Options available are:
  • Color Pathways in: Here, you may choose the color to use for highlighting the selected compound pathways. The default color is blue.
  • Display : If All Pathways is chosen, it shows all the pathways. However, the selected compound pathways are highlighted with the chosen color. The other pathways are drawn in black. If Only for Selected Compounds is chosen, only the selected compound pathways are drawn.

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SubGraphs

Subgraphs can be used to select compound and/or reaction nodes that will be grouped together. This allows you to draw the graph with certain nodes in close proximity to each other. After defining the subgraphs, you may assign compounds and reactions to them by the Subgraph column available in the Compounds and Reactions tabs respectively.
The properties for the subgraphs are detailed below:
  • The Name column denotes the name of the subgraphs.
  • The Cluster option is selected by default, so that the nodes that are assigned to the subgraph are shown inside a boundary box. By unselecting this option, the box is not drawn.
  • The Filled option is not selected by default. When selecting it and having the cluster option clicked, the background of the cluster box is filled with the color chosen in the following column.
  • The Fill Color allows you to choose the color for the background of the cluster box, provided that the Cluster option is selected. By default, LightCyan is enabled.
  • The Border Color indicates the color to be used for the edge of the cluster box, provided that the Cluster option is selected. Black is the default color.

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Compounds

Here, you may set some options for displaying the compound nodes in the reaction network.
  • The Hide column allows you to remove a selected compound from the reaction network graph.
    When the Display Pathway Traffic for Variable option is enabled, if you hide the compound and/or reaction node related to the highest traffic, the next busiest path will be drawn with the Max Arrow Width. The width increase factor will be displayed in the image on the Reaction Traffic node.
  • In the SubGraph column, you may assign compounds to a SubGraph.
  • The Rank allows you to define the relative placement for compounds nodes in the direction of the graph layout. The options available are same, min, source, max and sink.
    As an example, consider the case when Top->Bottom is selected as the Graph Direction. If two or more compounds are assigned to have same rank, they will be placed in the same vertical position. When source or sink is selected, they will be placed in the uppermost and lowermost locations respectively. Furthermore, compounds that are not ranked as source will be always placed below the source, and compounds that are not ranked as sink will be placed above the sink. When choosing min/max the placement has a similar effect as source/sink, except that other nodes may be located at the same vertical position.
  • The Fill Color column allows you to select the fill color for the chosen compound node. The coloring chosen is not applied when the Green-Fill Measured Species option is selected.
  • The Shape column displays some options for the shape of the compound nodes. The shape shown by default in the graph is ellipse for compound nodes. The shape chosen is not applied if the Green-Fill Measured Species option is selected.

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Reactions

This view has almost the same options as in the Compounds tab, except that they are applied to the reaction nodes.
One difference is that when choosing a color for a given reaction, the color is applied for all the arrows that come or leave the selected reaction node. To enable color selection for the reactions, you must disable the Highlight Pathway option.

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See Also:

Project Explorer

Formula

Reaction Traffic