Heat map

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A heat map is a graphical representation of data where the values
taken by a variable in a two-dimensional
map are represented as colors. A very similar presentation form is a tree map. The term is also used
to mean its thematic application as a
choropleth map.

Heat Maps originated in 2D displays of the values in a data matrix. Larger
values were represented by small dark gray or black squares (pixels) and smaller
values by lighter squares. Sneath (1957) displayed the results of a cluster analysis by
permuting the rows and the columns of a matrix to place similar values near each
other according to the clustering. Jacques Bertin used a
similar representation to display data that conformed to a Guttman
scale.The idea for joining cluster trees to the rows and columns of the data
matrix originated with Robert Ling in 1973. Ling used overstruck printer
characters to represent different shades of gray, one character-width per pixel.
Leland Wilkinson developed the first computer program in 1994 (SYSTAT) to produce a cluster
heatmap as a high-resolution color graphic. The Eisen et al. display shown in
the figure is a replication of the earlier SYSTAT design.

There are several different kinds of heat map.

Web heat maps have been used for displaying areas of a Web page most
frequently scanned by visitors. These have been incorporated in Web analysis
tools such as Google Analytics.

Heat map generated from DNA microarray data
reflecting gene expression values in several conditions

Biology heat maps are typically used in molecular biology to
represent the level of expression of many genes across a number of comparable
samples (e.g. cells in different
states, samples from different patients) as they are obtained from DNA microarrays.

The tree map is a 2D hierarchical
partitioning of data that visually resembles a heat map. They have been most
famously used in the Map of the Market applet featured on SmartMoney's website.

A mosaic plot is a tiled heat map for representing a two-way or higher-way
table of data. As with treemaps, the rectangular regions in a mosaic plot are
hierarchically organized. The means that the regions are rectangles instead of
squares. Friendly (1994) surveys the history and usage of this graph.

[edit]
References

Bertin, J. (1967).
Sémiologie Graphique. Les diagrammes, les réseaux, les cartes.
Gauthier-Villars.

Eisen, M.B., Spellman,
P.T., Brown, P.O. & Botstein, D. (1998). "Cluster
analysis and display of genome-wide expression patterns". Proc. Natl.
Acad. Sci. USA 95 (25): 14863–14868. doi:10.1073/pnas.95.25.14863. http://www.pnas.org/cgi/content/full/95/25/14863.  PMID 9843981 doi:10.1073/pnas.95.25.14863

Friendly, M. (1994). "Mosaic displays
for multi-way contingency tables". Journal of the American Statistical
Association 89: 190-200. http://www.math.yorku.ca/SCS/Papers/drew.

Ling,
R.F. (1973). "A computer generated aid for cluster analysis".
Communications of the ACM 16: 355–361.

Sneath, P.H.A. (1957). "The application of
computers to taxonomy". Journal of General Microbiology 17:
201–226.

Wilkinson, L. (1994). Advanced Applications:
Systat for DOS Version 6. SYSTAT Inc.. ISBN
9780134472850.

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Categories: Molecular
biology | Gene
expression | Bioinformatics
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This page was last modified on 30 January 2009, at 03:57.

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