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

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

## Pairwise comparisons of trees: Topological changes

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

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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.
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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?

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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.

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

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## 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?

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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.
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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?

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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
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?

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The nodes on the concentric circles clearly indicates the children, siblings or cousins of the node.
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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

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Slider bar is provided for controlling the node levels that are displayed on the screen.
Image:
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?

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It is clearly seen from the layout structure as the whole tree is shown at a glance.
Image:

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:

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)

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Strength (Treemap)
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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.
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In above image, we found that there is no node having HITCOUNT = 1175.

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

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Strength (Treemap)
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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.
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Nodes are filtered for MTIME and CTIME attributes.

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

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It is clearly seen from the layout structure as the whole tree is shown at a glance.
Image:
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)

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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.
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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

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

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## General visualization of trees: Labeling

### Review all the labels in a subtree

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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:
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

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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.
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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

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

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

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### Providing ways to permute links and nodes to verify hypotheses interactively

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Strength (3D Tree)
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Branch swapping is done by clicking on non-leaf node.
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### 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?

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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:

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:
In image 1, Search is done on 'Common Name', while in image 2, on 'Latin Name'.

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## File system and usage logs: Application specific tasks

### Where are the big directories?

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Strength (Treemap)
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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.
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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.

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

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Setting the color code attribute for Ctime (recently created webpages), we have the nodes highlighted for easy visual identification.
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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.

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