Advanced Heat Map and Clustering Analysis Using Heatmap3

Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr

研究成果: Article同行評審

116 引文 斯高帕斯(Scopus)

摘要

Heat maps and clustering are used frequently in expression analysis studies for data visualization and quality control. Simple clustering and heat maps can be produced from the "heatmap" function in R. However, the "heatmap" function lacks certain functionalities and customizability, preventing it from generating advanced heat maps and dendrograms. To tackle the limitations of the "heatmap" function, we have developed an R package "heatmap3" which significantly improves the original "heatmap" function by adding several more powerful and convenient features. The "heatmap3" package allows users to produce highly customizable state of the art heat maps and dendrograms. The "heatmap3" package is developed based on the "heatmap" function in R, and it is completely compatible with it. The new features of "heatmap3" include highly customizable legends and side annotation, a wider range of color selections, new labeling features which allow users to define multiple layers of phenotype variables, and automatically conducted association tests based on the phenotypes provided. Additional features such as different agglomeration methods for estimating distance between two samples are also added for clustering.

原文English
文章編號986048
期刊BioMed research international
2014
DOIs
出版狀態Published - 2014

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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