Diff for "GroupViews"

TableOfContents([2])

Proposal

The goal is to provide different ways of viewing a group of nodes of a network. We must provide a visualization that will present nodes with specific characteristics or similarities in a clear and organized manner without intrusion on the view of the rest of the network.

To accomplish this goal we will introduce use cases that will present a different type of group view that will provide an option for this feature.

Biological Questions / Use Cases

Use Case 1 - Single Node

Solution: A group of nodes can be visualized by collapsing the selected group (child nodes) into a single parent node. The connections that exist between the child nodes and the surrounding nodes of the network will be represented in this view. All the edges connected to the child nodes will be connected to the single parent node.

Characteristics: The group node will have the option of having specific characteristics that will help in representing the child nodes. For example if the color of the child nodes was an important feature in the network, the parent node can inherit a color that will be more helpful in representing the child nodes within. This can be done by using a color value that is an average of all the color values of the child nodes, or use a color value that appears the most frequent within the group.

Visualization: The user can have the ability to view information within the node without expanding the group node. A tool tip window can appear when a cursor moves over the group node and a list of names of all the child nodes can appear in the window. Other important information can also appear in this window, such as a list (or a percentage figure if the number child nodes is large) of the type of nodes that exist in this group or other features such as color if necessary.

Visual Aid:

Use Case 2 - Bounding Box

Solution: A group of nodes can be visualized by a bounding box. This box will have the ability to move around and as a result move the child nodes along with it. Surrounding nodes of the network can then be dragged and dropped into the bounding box and will behave as child nodes.

Characteristics: The bounding box can have different appearances that can represent different types of groups (from a biological standpoint). For example the bounding box may appear as a simple rectangular frame or a circle or a set of brackets and a legend can explain the associations.

Visualization: All the child nodes will be clearly visible along with their characteristics as they were before the grouping.

Visual Aid:

Use Case 3 - New Network Window

Solution: Represent a group of nodes by a single parent node but during expanded view, show the child network in a new window.

Characteristics: The single parent node can have its own characteristics, such as those described in Use Case 1. A “+’ symbol will appear when the mouse is moved over a parent node and when clicked, a window will pop-up that will show the child nodes as a new network.

Visual Aid:

Use Case 4 - Stacked View

Solution: A matrix view of the group nodes that is represented using a vertical stacking of child nodes. During collapsed view, the child nodes are represented by a single parent node, such as in Use Case 1. During expanded view (stacked), the child nodes will be shown vertically stacked.

Characteristics: During stacked view, different sections of a single node can be viewed and each section of the node will have edges connected to it.

Visualization: Each section of the node will be presented by a block and each block will be stacked on top of each other to represent a single node. Each block can be differentiated with a name and a separate color.

Visual Aid:

General Notes

Requirements

Deferred Items

Open Issues

Backward Compatibility

Expected growth and plan for growth

References

Implementation Plan

Comments

• Idea: layout of biological pathways where network motifs (e.g. a biochemical reaction) is represented as a group, the groups are layed out, then the groups/motifs are viewed as they would be in a textbook e.g. biochemical reactions would be viewed as they are in textbooks. This would include the ability to apply a standard layout to members of a group and view the result.

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