Abstract
BackgroundThe graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expression levels, such as those measured with RNAseq and microarray experiments, to provide qualitative large-scale views of the transcriptonomic landscape. Creating high-quality heatmaps is a computationally intensive task, often requiring considerable programming experience, particularly for customizing features to a specific dataset at hand.MethodsSoftware to create publication-quality heatmaps is developed with the R programming language, C++ programming language, and OpenGL application programming interface (API) to create industry-grade high performance graphics.ResultsWe create a graphical user interface (GUI) software package called HeatmapGenerator for Windows OS and Mac OS X as an intuitive, user-friendly alternative to researchers with minimal prior coding experience to allow them to create publication-quality heatmaps using R graphics without sacrificing their desired level of customization. The simplicity of HeatmapGenerator is that it only requires the user to upload a preformatted input file and download the publicly available R software language, among a few other operating system-specific requirements. Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge.ConclusionWe provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R. The software is available for Microsoft Windows and Apple Mac OS X. HeatmapGenerator is released under the GNU General Public License and publicly available at: http://sourceforge.net/projects/heatmapgenerator/. The Mac OS X direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_MAC_OSX.tar.gz/download. The Windows OS direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_WINDOWS.zip/download.
Highlights
The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research
The graphical user interface (GUI) is written in FLTK [8], a cross-platform object-oriented widget toolkit written in the C++ programming language with an interface to OpenGL
Running the HeatmapGenerator software package produces a variety of heatmaps showing the relative expression levels of genes from either large or small datasets used as the input to the program
Summary
The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. In the medical research community, heatmaps are used to comparatively illustrate gene expression levels across a number of different samples (e.g., cells under different experimental conditions or samples from different patients) obtained from DNA microarray studies or high-throughput sequencing methods such as RNAseq. There is an abundance of such services, none of them boast comparable graphical capabilities such as those produced by the R programming language: popularly considered to be one of the most powerful and widely used statistical software among researchers in the medical community and the lingua franca for preparing heatmaps for publication. The GUI of HeatmapGenerator is the first software of its kind to employ a database storage system that stores a user’s previously generated heatmaps, in case the user wishes to go back to retrieve them from memory or compare them to other generated heatmaps, all within a central repository
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