InfoVis 2003 Contest - Treemap, Radial Tree and 3D Tree Visualizations

Nihar Sheth
School of Informatics
Indiana University, Bloomington
nisheth@indiana.edu
Katy Börner, Jason Baumgartner & Ketan Mane
School of Library and Information Science
Indiana University, Bloomington
 
{katy, jlbaumga, kmane} @indiana.edu
Eric Wernert
Computer Science Department
Indiana University, Bloomington
ewernert@cs.indiana.edu

This page is generated according to the Infovis 2003 Contest rules and tasks at http://www.cs.umd.edu/hcil/iv03contest/

Ratings used below: (Strength, Possible, Difficult, Not Available)

Pairwise comparisons of trees: Topological changes

Did anything change, in general, or in a subtree?

Rating:
Possible (3D Tree)
Process:
          In the 3D Tree Viewer, the change in the structure of the phylogenetic trees is reflected if unidirectional links for leaf nodes of a sub-tree are linked to different sub-trees of the comparison tree.
Image:

Answer:  
           There are some dissimilarities between the two trees (above image) when we try to match the leaf nodes between two trees, matching leaf nodes exist in other sections of the tree.

What nodes were added, deleted?

Rating:
Possible (3D Tree)
Process:
           In 3D tree viewer, if nodes are added or deleted in a tree, and when we try to establish the links between leaf nodes of the tress, then  we will not find links for those nodes. Thus, we can tell that there is a addition or deletion in either of the tree.
 
Image:

Answer:
In given phylogenetic trees, no nodes are added or deleted.

Did any node or subtrees "move" in the tree? Can you characterize those movements?

 
Rating:
Not Available
Process:
         N/A
Image:
N/A
Answer:
N/A

Pairwise comparisons of trees: Attribute value changes

Global impression: did things change a lot or not?

 
Rating:
Not Available
Process:
         N/A
Image:
N/A
Answer:
N/A

What nodes or subtrees changed the most?

 
Rating:
Not Available
Process:
         N/A
Image:
N/A
Answer:
N/A

Did the value of attribute XYZ for this node increase or decrease? In absolute terms, or relatively to other siblings or other nodes.

 
Rating:
Not Available
Process:
         N/A
Image:
N/A
Answer:
N/A

General visualization of trees: Topology

Overall characteristics: How large is the tree? How many levels deep? What is the deepest branch? Does the depth vary between subtrees or not?

Rating:
Strength (Radial tree viewer)
Process:
Radial tree is displayed over concentric circles in the background. The root node is located at the center and rest of the nodes are allocated on different circles depending on their hierarchical level. A fish-eye overview shows the topology of the tree. The presence of the node on the farthest circle indicates it level and deepness in the structure. The depth-ness is explicitly clear from the structural layout of the tree.
Image:
Answer:
        By looking at above image, one can tell that the tree is very large. One can manually count the levels. One can easily tell the depth differences for subtrees.

Path: What is the path of this node?

Rating:
Strength (Radial tree viewer)
Process:
        When a node is selected that node comes to the center of the concentric circles. The path from this node to the root node is drawn in black color, which is easily distinguished from the other path links.
Image
Answer:
        In above image, path of node "Cebidae"  can be traced as "Cebidae < Primates < Eutheria < Theria < Mammalia".

Local relatives: What are the children, siblings, or cousins of this node?

Rating:
Strength (Radial tree viewer)
Process:
The nodes on the concentric circles clearly indicates the children, siblings or cousins of the node.
Image:
Answer:
The nodes are arranged on the concentric circles based on their hierarchical structure and hence the relations can be clearly established.

Filtering by level: Show only the first level, or show only 3 levels down, or remove all the leaves

Rating:
Strength (Radial tree viewer)
Process:
Slider bar is provided for controlling the node levels that are displayed on the screen.
Image:
   
Answer:
In 1st image, nodes till first 10 levels of "Primates" subtree are displayed. In 2nd and 3rd image, nodes till first 4 and first 2 levels of "primates" subtree are displayed.

Topologies question that involve counting nodes can be seen as attribute dependant questions: e.g. Which branch contains the largest number of nodes? or Which branch has the largest fan-out?

Rating:
Strength (Radial tree viewer)
Process:
It is clearly seen from the layout structure as the whole tree is shown at a glance.
Image:
 
Answer:
        In above image, 'Primates' subtree is displayed. In 'Primates' subtree, 'Cebidae' subtree contains the largest number of nodes in this subtree.

General visualization of trees: Attribute based

Find nodes with high values of a numerical attribute X? (relative query)

Rating:
Strength (Treemap)
Process:
Filter slider bars are available for all numerical attributes.  Dynamic filtering is achieved through control of sliders. 
 Image:
 
Answer:

        In left image, nodes are filtered for HITCOUNT having more than 1000. In right image, nodes are filtered for CTIME attribute.

Find nodes with given value of a numerical attribute X? (absolute query)

Rating:
Strength (Treemap)
Process:
The filter sliders can be used to set the threshold range values for the filtering nodes. By setting the lower and higher threshold to the given value, we can identify the nodes with a given value of a numerical attribute X.
 Image:
Answer:
In above image, we found that there is no node having HITCOUNT = 1175.

Find nodes with value Y of categorical attribute X - What value of a categorical attribute occurs more often? e.g. Are there more farm animals or pets?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Find nodes with certain values of two or more attributes (What video file is used the most?)

Rating:
Strength (Treemap)
Process:
Filter slide bars can be used for more than one attribute simultaneously for finding the nodes. This is very much possible for only numerical attributes.
Image:
Answer:
Nodes are filtered for MTIME and CTIME attributes.

Number of nodes in a tree or subtree? (How many animals? How many mammals?)

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Comparison of branches of the tree (Subtrees with most nodes; are there more mammals or fish?)

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Largest fanout (What is the largest group of animals with same lineage?)

Rating:
Strength (Radial tree viewer)
Process:
It is clearly seen from the layout structure as the whole tree is shown at a glance.
Image:
Answer:
       From above image, one can easily identify that 'Primates' is the largest group in 'Eutheria' subtree.

General visualization of trees: Known items

Which nodes have a particular string in their label? (Find "giraffe" in a tree of animals)

Rating:
Strength (Radial tree viewer)
Process:
Search feature is provided to locate the node having the query string. The search function supports the regular expression features too. Matching nodes are highlighted.
Image:
Answer:
        Animals with 'giraffe' string in their label is not in 'Mammal' subtree. In above image, you can see the search results of 'dolphin'.

Locate a node knowing its path

Rating:
Strength (Radial tree viewer)
Process:
Radial tree supports the hierarchical data structure very well. So by having parent-child relationship knowledge, one can easily locate the desired node.
Image:
Answer:
        In above image, we located the animal 'rats'. We can directly reach that by using Search feature also.

Go back to a node you have visited before

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

General visualization of trees: Labeling

Review all the labels in a subtree

Rating:
Strength (Treemap, Radial tree viewer)
Process:
In treemap, every node is given a label. However if the node is not large enough to clearly display its label then the label is seen in the tooltip obtained by hovering the mouse over the node.
In radial tree viewer, label display is on at the first level only for clear visibility of the labels. Similar to the treemap, the labels for the rest of the  nodes are available in the tooltip.
Image:
   
Answer:
        It is clearly seen from the above images.

General visualization of trees: Browsing

Explore the tree by performing a series of up and downs in the tree

Rating:
Strength (Treemap, Radial tree viewer)
Process:
In treemap, clicking the parent node displays the children nodes that are present. For radial tree, we see that if the node of interest has children nodes then they are arranged in the fanout fashion at their respective levels.
Image:
       
Answer:
        In radial tree, One can do tree browsing by clicking on parent-child nodes. In treemap, one can go down in the tree by clicking on node, while to go up, one needs to right-click on high-level of visible parent node.

General visualization of trees: Managing the analysis

Marking nodes of interest

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Removing special anomalies

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Saving visualization settings for future reference

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Keeping the history of your analysis, reviewing it and replaying it with different parameters

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Phylogenies: Application specific tasks

The higher-level problem is to find the best way to map the similarities between the two trees topologies, which would indicate co-evolution, and, maybe, the point(s) where the two proteins were not co-evolving. Is there Co-evolution?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Interacting with the tree matching process to solve inconsistencies

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Displaying the trees, with or without taking into account the branch length (the length of the links)

Rating:
Strength (3D Tree)
Process:
          This tool provides us with an option to consider/not consider the branch length while displaying the tree.
Image:
Answer:
        In above image, branch length is considered while displaying the tree.

Showing the relationships and differences from a computed or interactively constructed mapping

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Providing ways to permute links and nodes to verify hypotheses interactively

Rating:
Strength (3D Tree)
Process:
Branch swapping is done by clicking on non-leaf node.
Image:
Answer:
       

Classifications: Application specific tasks

To what extent are the differences in the classifications due to differences in how animals are thought to be related? Are there other kinds of differences and can you explain them?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Can you say in how many different subtrees a particular common name (such as "dolphin" or "horse") is used? How closely are these animals related? Are common names a good guide to understanding relationships?

Rating:
Possible
Process:
Using the search feature, query can be submitted to highlight the nodes.  Thus making it easy to identify how many trees have the query term.
Image:
  
Answer:
        In above image, nodes in black color have 'dolphin' in their common name. From the display, one can tell that all these nodes are part of 'Odantoceti' subtree.

How many species or subspecies are named after biologists named "Townsend"?

Rating:
Possible
Process:
Using the search feature, query can be submitted to highlight the nodes.  Thus making it easy to identify how many trees have the query term.
Image:
   
Answer:
        In image 1, Search is done on 'Common Name', while in image 2, on 'Latin Name'.

What kind of feedback does your tool provide to alert the user quickly when a wrong name is entered?

Rating:
Not available
Process:
N/A
Image:
 
N/A
Answer:
N/A

For the top five subtrees with the most nodes-- are they likely to have a parent of a particular rank? Or does this happen in many ranks? Can you comment on how useful "rank" is?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

File system and usage logs: Application specific tasks

Where are the big directories?

Rating:
Strength (Treemap)
Process:
In treemap, we can use any size attribute value to set the node size. Thus we can view the big directories based on the size attribute value.
Image:
       
Answer:
        Directories /movies, /projects/SoftEng/ESEG (big in projects dir), /users/gasarch( big in user dir), /classes/spring2002/cmsc828g are big directories in their parent directories respectively.

Can you see different patterns in the files? (Can you make out the difference between personal pages, class pages and research project pages?)

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Were there a lot of pages created recently? If so, in which part of the file system?

Rating:
Strength
Process:
Setting the color code attribute for Ctime (recently created webpages), we have the nodes highlighted for easy visual identification.
Image:
       
Answer:
        Nodes with light blue color are recently created. One can observe that most of these recently created files are index.html and they are scattered throughout the / directories.

Are the newer directories bigger than the older projects?

 
Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

When was the page giving directions to the department last updated?

 
Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Which are the popular webpages?

 
Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Are there some labs more popular than others?

 
Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Which areas are getting more popular? Less popular?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Are new pages more popular that old pages?

 
Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Which old pages are popular?

 
Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

What proportion of the pages are never used?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

What proportion of the pages are seldom used?

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Other Strengths of the System

<Task Name>

Rating:
Not available
Process:
N/A
Image:
N/A
Answer:
N/A

Web Accessibility