HemI: A Toolkit for Illustrating Heatmaps

TLDR

High‑throughput technologies generate vast biological datasets, and heatmaps provide a concise, comprehensive way to visualize gene or protein expression dynamics across conditions. This study introduces HemI, an easy‑to‑use tool designed to generate heatmaps from gene or protein expression data. HemI, implemented in Java, offers customizable heatmap rendering—including recoloring, rescaling, and rotation—alongside multiple clustering strategies and direct export of publication‑quality figures. The authors demonstrate that HemI serves as a practical toolkit for efficiently visualizing and manipulating heatmaps.

Abstract

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.