The Fundamentals of Constructing and Interpreting Heat Maps

  • Nathaniel M. VacantiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1862)


This chapter is intended to introduce the fundamental principles of the heat map, the most widely used medium to present high-throughput data, to scientists unaccustomed to analyzing large data sets. Its scope includes describing the general features of heat maps, how their components are designed, the meaning of parameters such as “distance method” and “linkage method,” and the influence of manipulations such as row-scaling and logarithmic transformations on data interpretation and presentation. This chapter may serve as a guide to understanding the use of heat maps in published analyses or to aid in their design, allowing efficient interpretations of high-throughput experiments, exploration of hypotheses, or clear communications of findings.

Key words

Heat map Dendrogram Hierarchical clustering Linkage method Correlation 


  1. 1.
    Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtio J (2018) Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun 9(1):903. CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtio J (2017) Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. Sci Rep 7(1):4513. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58(301):236–244. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Division of Nutritional SciencesCornell UniversityIthacaUSA
  2. 2.Department of Oncology-Pathology, Science for Life LaboratoryKarolinska InstitutetStockholmSweden

Personalised recommendations