Stanford Medicine

Tools & Scripts

Heatmap Builder

A common approach to the visualization of ‘large number’ experiments in genomics is the representation of microarray data points as boxes of different color shades. We have developed a standalone application for generating such images (‘heatmaps’) in Visual C# using the .NET environment. The program offers dataset-normalized and row-normalized algorithms for color allocation, and pre-determined or linear-morphing algorithms for color selection. Data points are represented either by filled boxes, or by boxes filled with a circle or rectangle with an area proportional to the data point value. Several output formats are available, including standard compression algorithms and lossless file formats.

To download our heatmap builder, please first send a courtesy email to Dr. Ashley then download the file. Please change the extension of .123 to .exe. You can also access a sample input file for the heatmap builder. For methods (and reference in the case of publication) please see:

King JY, Ferrara R, Tabibiazar R, Spin JM, Chen MM, Kuchinsky A, Vailaya A, Kincaid R, Tsalenko A, Deng DX, Connolly A, Zhang P, Yang E, Watt C, Yakhini Z, Ben-Dor A, Adler A, Bruhn L, Tsao P, Quertermous T, Ashley EA. Pathway analysis of coronary atherosclerosis. Physiol Genomics. Sep 21 2005;23(1):103-118. pdf