NeatMap - non-clustering heat map alternatives in R

Background: The clustered heat map is the most popular means of visualizing genomic data. It compactly displays a large amount of data in an intuitive format that facilitates the detection of hidden structures and relations in the data. However, it is hampered by its use of cluster analysis which does not always respect the intrinsic relations in the data, often requiring non-standardized reordering of rows/columns to be performed post-clustering. This sometimes leads to uninformative and/or misleading conclusions. Often it is more informative to use dimensionreduction algorithms (such as Principal Component Analysis and Multi-Dimensional Scaling) which respect the topology inherent in the data. Yet, despite their proven utility in the analysis of biological data, they are not as widely used. This is at least partially due to the lack of user-friendly visualization methods with the visceral impact of the heat map. Results: NeatMap is an R package designed to meet this need. NeatMap of...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Satwik Rajaram, Yoshi Oono
• Keywords: BMCBI 2010, Cluster Analysis, Heat Map, Principal Component Analysis