Good Visualization

 

Kerstin Lindblad-Toh, Claire M Wade, Tarjei S. Mikkelsen, Elinor K. Karlsson, David B. Jaffe, Michael Kamal, Michele Clamp, Jean L. Chang, Edward J. Kulbokas, III, Michael C. Zody, Evan Mauceli, Xiaohui Xie, Matthew Breen, Robert K. Wayne, Elaine A. Ostrander, Chris P. Ponting, Francis Galibert, Douglas R. Smith, Pieter J. deJong, Ewen Kirkness, Pablo Alvarez, Tara Biagi, William Brockman, Jonathan Butler, Chee-Wye Chin, April Cook, James Cuff, Mark J. Daly, David DeCaprio, Sante Gnerre, Manfred Grabherr, Manolis Kellis, Michael Kleber, Carolyne Bardeleben, Leo Goodstadt, Andreas Heger, Christophe Hitte, Lisa Kim, Klaus-Peter Koepfli, Heidi G. Parker, John P. Pollinger, Stephen M. J. Searle, Nathan B. Sutter, Rachael Thomas, Caleb Webber and Eric S. Lander (2005). Genome sequence, comparative analysis and haplotype structure of the domestic dog.  Nature 438, pp. 803-819.

 

Available at http://www.nature.com/nature/journal/v438/n7069/full/nature04338.html

 

 

Original Figure Caption:  The phylogenetic tree is based on approx15 kb of exon and intron sequence (see text). Branch colours identify the red-fox-like clade (red), the South American clade (green), the wolf-like clade (blue) and the grey and island fox clade (orange). The tree shown was constructed using maximum parsimony as the optimality criterion and is the single most parsimonious tree. Bootstrap values and bayesian posterior probability values are listed above and below the internodes, respectively; dashes indicate bootstrap values below 50% or bayesian posterior probability values below 95%. Horizontal bars indicate indels, with the number of indels shown in parentheses if greater than one. Underlined species names are represented with corresponding illustrations. (Copyright permissions for illustrations are listed in the Supplementary Information.) Divergence time, in millions of years (Myr), is indicated for three nodes as discussed in ref. 1. For scientific names and species descriptions of canids, see ref. 119. A tree based on bayesian inference differs from the tree shown in two respects: it groups the raccoon dog and bat-eared fox as sister taxa, and groups the grey fox and island fox as basal to the clade containing these sister taxa. However, neither of these topological differences is strongly supported (see text and Supplementary Information).

 

The above figure is a phylogenetic tree of canine species demonstrating speciation over time and genetic similarities between groups.  The x-position illustrates when speciation occurred, and what species derive from this speciation.  When information is available, phylogenetic trees often display evolution times according to y-position (this was not possible in the present diagram).  Colour is frequently used to illustrate species groupings or categorical traits held by species.  This particular tree is based on exon and intron sequences and demonstrates the probable evolutionary branching that occurred.  This data representation is typical of modern phylogenetic trees with all living species aligned with one another, speciation represented by branching lines, and genetic diversity and similarity implicitly represented by the branching order, and the physical proximity of one species to another.  Many phylogenetic trees provide statistical support for their chosen orderings.  Branching order for this figure was determined by two means: bootstrapping and Bayesian posterior probability values.  Dashes in place of a number indicate that the bootstrap values were below 50% or the Bayesian posterior probability was below 95% (the chances that such genetic similarity is by chance is less than 5%).  Branch colours allow the reader to quickly categorize and group canine species.  Finally, species illustrations are provided on the far right to illustrate what animals from each group look like.  Illustrations correspond with underline species names of matching colour and approximately matching y-position.  Known evolutionary dates are individually identified.

 

 

As stated above, this figure is a fairly typical phylogenetic tree. Phylogenetic trees are a traditional way that evolutionary biologists can quickly and clearly group animal species by evolutionary history (based on species proximity), illustrate common ancestors (where branching between species occurs), and visually illustrate genetic disparity between species (the number of branches between species).  The x-position of any speciation event can also correspond with a time scale in some phylogenetic trees.   Appropriately, there is no hierarchy amongst modern species.  For this particular tree, the statistical justification for the given branching order is provided, and line colours enable the reader to quickly group species.  Finally, this visualization is appropriate for its target audience.  Nature is not a journal exclusive to biologists so common names are used and illustrations are provided.  These illustrations also provide an informal means of comparison between species.  Speciation timelines are probably not known for each branching event.  Individual known speciation times are thus identified individually.

 

 

 

Bad Visualization

 

Hilmer, G., Elliott, G., Cunliffe, D. and D. Tudhope (2000).  Open educational hypermedia systems: an n-dimensional framework for user profile interchange. In proceedings of EDMEDIA 2000, Montreal, 2000. 

Abstract viewable at http://www.editlib.org/index.cfm?CFID=32335993&CFTOKEN=79248554&fuseaction=Reader.ViewAbstract&paper_id=16107

 

 

This figure seems to have little or nothing to do with the accompanying article.  Hilmer et al.’s work discuses Educational Hypermedia Systems and how modeling user knowledge can help the system to be more pedagogical effective.  The authors discuss “dimensions” of user modeling, and how to share user models between systems that require different dimensionality.  The above figure was preceded with the following statement: “The following chart visualizes our n-dimensional mapping approach of UPI in OHES:”.  OEHS stands for Open Educational Hypermedia Systems (the authors seem to have inverted two letters), UPI is User Profile Interchange and AHS is an acronym for Adaptive Hypermedia Systems.   This chart seems to be trying to demonstrate how user model dimensionality can be changed from one application to another.

 

The above figure does not really display any real information, despite its large size.  One axis is unlabelled while the other does not clearly articulate any information other than graphically displaying 5 levels along the y-axis.  The x-axis is assumed to also be showing AHS dimensions, although this is not actually illustrated.  Neither axis has the dimension numbers labeled nor is it clear why the top and right sides of the chart are terminated with a curved line.  The purpose of this chart seems to be to show how user model dimensionality can be changed from one application to another, but this visualization doesn’t demonstrate how this occurs.  This chart really doesn’t seem necessary in any way.