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
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?
