title: Advanced heat map and clustering analysis using heatmap3.
abstract: 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.
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Shilin
authors.identifier: 0000-0002-3787-8111
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Yan
authors.identifier: 0000-0001-5252-3960
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Quanhu
authors.identifier: 0000-0001-8951-9295
authors.initials: Q
authors.lastname: Sheng
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Yu
authors.identifier: 0000-0003-2086-9670
authors.initials: Y
authors.lastname: Shyr
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics; D016000:Cluster Analysis; D030541:Databases, Genetic; D005260:Female; D052138:Genes, Neoplasm; D023281:Genomics / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation; D012984:Software