Advanced Heat Map and Clustering Analysis Using Heatmap3


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 function in R. However, function lacks certain functionalities and customizability, preventing it from generating advanced heat maps and dendrograms. To tackle the limitations of function, we have developed an R which significantly improves the function by adding several more powerful and convenient features. package allows users to produce highly customizable state of the art heat maps and dendrograms. package is developed based on function in R, and it is completely compatible with it. The new features 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.


R package heatmap3 can be found at cran.


Zhao, S., Y. Guo, Q. Sheng and Y. Shyr, 2014 Advanced heat map and clustering analysis using heatmap3. Biomed Res Int 2014: 986048.