HemI: a toolkit for illustrating heatmaps

PLoS One. 2014 Nov 5;9(11):e111988. doi: 10.1371/journal.pone.0111988. eCollection 2014.


Recent high-throughput techniques have generated a flood of biological data in all aspects. The transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. In this work, we developed an easy-to-use tool named HemI (Heat map Illustrator), which can visualize either gene or protein expression data in heatmaps. Additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. In addition, HemI provides multiple clustering strategies for analyzing the data. Publication-quality figures can be exported directly. We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps. The stand-alone packages of HemI were implemented in Java and can be accessed at http://hemi.biocuckoo.org/down.php.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cluster Analysis
  • Computational Biology / methods*
  • Gene Expression Profiling / methods
  • Software*

Grants and funding

The work was supported, in whole or in part, by the National Basic Research Program (973 project) (2012CB910101, and 2013CB9339002), Natural Science Foundation of China (31171263, 81272578 and J1103514), International Science & Technology Cooperation Program of China (2014DFB30020), China Postdoctoral Science Foundation (2014M550392), and Fundamental Research Funds for the Central Universities (HUST: 2013TS080, 2014YQ003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.