Visualizing gene clusters using neighborhood graphs in R



Publication Details

Scharl, T. & Leisch, F. (2008). Visualizing gene clusters using neighborhood graphs in R. In P. Brito (Eds.), Compstat 2008-Proceedings in Computational Statistics (pp. 51-58). Heidelberg, Germany: Physica Verlag.


The visualization of cluster solutions in gene expression data analysis gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results. Neighborhood graphs allow for visual assessment of relationships between adjacent clusters. The number of clusters in gene expression data is for biological reasons rather large. As a linear projection of the data into 2 dimensions does not scale well in the number of clusters there is a need for new visualization techniques using non-linear arrangement of the clusters. The new visualization tool is implemented in the open source statistical computing environment R. It is demonstrated on microarray data from yeast.

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Computational Statistics Symposium

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