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|| '''RFC Name''' : Group views || '''Editor(s)''': Anna Rukosuyeva || '''Status''': Being written || |
||'''RFC Name''' : Group views ||'''Editor(s)''': Anna Rukosuyeva ||'''Status''': Being written || |
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| 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. | |
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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. |
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=== Use Case 1 - Single Node === |
=== Grouped Visualization 1 - Single Node === |
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| '''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. | '''Characteristics:''' The group node will have the option of having specific characteristics that will help in representing the chilf nodes. |
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| '''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. | ''Average:'' 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. |
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| '''Visual Aid:''' | |
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| === Use Case 2 - Bounding Box === | ''Pie Chart:'' The group characteristics can also be represented by a pie chart. The pie chart can show segments of the colors that the child nodes represent, the size of each segment will be representative of how often that color appears in the child nodes. An implementation of this idea exists and can be found at: http://genepro.ccb.sickkids.ca/screenshots.html |
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''Tool Tip:'' 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. '''Use Cases:''' ''Use Case 1'' "Clustering-Biomodules" [http://www.cytoscape.org/cgi-bin/moin.cgi/groupAPI/UseCase_1] ''Use Case 2'' "Protein Complexes–Pico/GenMAPP" [http://www.cytoscape.org/cgi-bin/moin.cgi/groupAPI/UseCase_2A] === Grouped Visualization 2 - Bounding Box === |
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| '''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. | '''Characteristics:''' All the child nodes will be clearly visible along with their characteristics as they were before the grouping. The characteristics of the bounding box can change to reflect different characteristics of the group nodes. |
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| '''Visualization:''' All the child nodes will be clearly visible along with their characteristics as they were before the grouping. |
''Box Shape:'' The shape of the bounding box can change to the shape that the grouped nodes make. ''Different Box Shape:'' 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. ''Width of Box:'' The width of the border of the bounding box can change with the number of nodes that are inside the group. ''Box Location:'' To avoid clutter and show a clear distinction between the grouped nodes and the rest of the network, the bounded group should be moved to a separate, empty part of the network panel. An implementation of this idea named the '''“Bubble Router”''' can be found at:[http://conklinwolf.ucsf.edu/genmappwiki/Bubble_Router_Plugin] '''Use Cases:''' === Expanded View Visualization 1 – Staked View === '''Solution:''' After expanding the grouped nodes, show the child nodes as 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. 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. |
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| === Use Case 3 - New Network Window === |
=== Expanded View Visualization 2 – New Window === '''Solution:''' After expanding the grouped nodes, show the child nodes as a new network in a separate window. |
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'''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. |
'''Characteristics:''' A “+’ symbol will appear when the mouse is moved over a parent node and when clicked, a new network window pop-up that will show the child nodes as a new network. |
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| === Use Case 4 - Stacked View === |
=== Expanded View Visualization 3 – Group Panel === '''Solution:''' For each grouped visualization described above, create a group panel in Cytoscape that will show a more detailed, hierarchical structure of the group. This panel will be very helpful when the groups become more complex with multiple levels of parent nodes. |
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'''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. |
'''Characteristics:''' The parent node will be listed in the panel with all the child nodes and their characteristics branching from it. This view will be very similar to Windows Explorer that shows the file hierarchy. |
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| '''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''' |
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| '''Visual Aid:''' |
=== Expanded View Visualization 4 – Tree Map === '''Solution:''' A hierarchical node grouping can be flattened out and shown as a birds-eye, textual representation. '''Characteristics:''' This view will work for groups that can be represented by trees, ie: multiple parent nodes can exists, but none of the parent nodes can share any child nodes. '''Visual Aid:''' An example of this type of presentation can be seen here: === Expanded View Visualization 5 – Mouse-Over Tool === '''Solution:''' Create a viewing tool that will be controlled by a mouse and will travel over the network panel, when the tool moves over a parent node, the inside of the parent node. '''Characteristics:'''This tool will show an “x-ray”, detailed view of the inside of the parent node. '''Visual Aid:''' An example of this type of tool can be seen here: |
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'''Converting Between Visualizations''' The user should be able to convert from one type of a visualization to another with a simple mouse click. |
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Mapping Node Attributes to Nodes Mapping Edge Attributes Parent nodes share the same child nodes |
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| * 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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| Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. '''Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.''' | Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. '''Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.''' |
RFC Name : Group views |
Editor(s): Anna Rukosuyeva |
Status: Being written |
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
Grouped Visualization 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 chilf nodes.
Average: 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.
Pie Chart: The group characteristics can also be represented by a pie chart. The pie chart can show segments of the colors that the child nodes represent, the size of each segment will be representative of how often that color appears in the child nodes. An implementation of this idea exists and can be found at: http://genepro.ccb.sickkids.ca/screenshots.html
Tool Tip: 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.
Use Cases:
Use Case 1
"Clustering-Biomodules" [http://www.cytoscape.org/cgi-bin/moin.cgi/groupAPI/UseCase_1]
Use Case 2
"Protein Complexes–Pico/GenMAPP" [http://www.cytoscape.org/cgi-bin/moin.cgi/groupAPI/UseCase_2A]
Grouped Visualization 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: All the child nodes will be clearly visible along with their characteristics as they were before the grouping. The characteristics of the bounding box can change to reflect different characteristics of the group nodes.
Box Shape: The shape of the bounding box can change to the shape that the grouped nodes make.
Different Box Shape: 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.
Width of Box: The width of the border of the bounding box can change with the number of nodes that are inside the group.
Box Location: To avoid clutter and show a clear distinction between the grouped nodes and the rest of the network, the bounded group should be moved to a separate, empty part of the network panel.
An implementation of this idea named the “Bubble Router” can be found at:[http://conklinwolf.ucsf.edu/genmappwiki/Bubble_Router_Plugin]
Use Cases:
Expanded View Visualization 1 – Staked View
Solution: After expanding the grouped nodes, show the child nodes as 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. 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:
Expanded View Visualization 2 – New Window
Solution: After expanding the grouped nodes, show the child nodes as a new network in a separate window.
Characteristics: A “+’ symbol will appear when the mouse is moved over a parent node and when clicked, a new network window pop-up that will show the child nodes as a new network.
Visual Aid:
Expanded View Visualization 3 – Group Panel
Solution: For each grouped visualization described above, create a group panel in Cytoscape that will show a more detailed, hierarchical structure of the group. This panel will be very helpful when the groups become more complex with multiple levels of parent nodes.
Characteristics: The parent node will be listed in the panel with all the child nodes and their characteristics branching from it. This view will be very similar to Windows Explorer that shows the file hierarchy.
Visual Aid
Expanded View Visualization 4 – Tree Map
Solution: A hierarchical node grouping can be flattened out and shown as a birds-eye, textual representation.
Characteristics: This view will work for groups that can be represented by trees, ie: multiple parent nodes can exists, but none of the parent nodes can share any child nodes.
Visual Aid: An example of this type of presentation can be seen here:
Expanded View Visualization 5 – Mouse-Over Tool
Solution: Create a viewing tool that will be controlled by a mouse and will travel over the network panel, when the tool moves over a parent node, the inside of the parent node.
Characteristics:This tool will show an “x-ray”, detailed view of the inside of the parent node.
Visual Aid: An example of this type of tool can be seen here:
General Notes
Converting Between Visualizations
- The user should be able to convert from one type of a visualization to another with a simple mouse click.
Requirements
Deferred Items
Open Issues
- Mapping Node Attributes to Nodes Mapping Edge Attributes Parent nodes share the same child nodes
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.
How to Comment
Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.