Heatmap Illustrator (HemI) Software

In this work, we presented a novel software package of HemI (Heatmap Illustrator, version 1.0), which used a red, green, and blue tricolor in a 256 color mode. Given a selected color scale, the total color space will be automatically processed into a numerical matrix (768 rows * 3 columns) by Java. Then the inputted gene or protein expression data can be linearly normalized as below: More frequently, researchers prefer to visualize the logarithmic relations between different conditions and molecular expression levels. Thus, the original data can also be normalized as below: While
In both equations, the Max cannot be equal to Min, and both OV and Min values must be greater than 0 in Eq. 2. The calculated NVs were then mapped to the color matrix, while the tricolor values of the nearest number of rows were visualized.
For further analysis of the data in heatmaps, several clustering approaches such as the hierarchical and k-means clustering algorithms, were also integrated. To calculate the distance, three types of linkage criteria (Table 3) and seven kinds of metrics (Table 4) were adopted for the two algorithms, respectively.
HemI 1.0 was written in Java 1.6 (J2SE 6.0) and packaged with Install4j 4.0.8. We developed six packages to support three major ×86/×64 operating systems (OSs), including Windows, Unix/Linux, and Mac. The stability and applicability of HemI was rigorously tested under Windows XP/7, Ubuntu, and Apple Mac OS X 10.5 (Leopard).