Abstract
BackgroundTwo-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions. Such "color-grid" representations have found increasing use in the biological sciences (e.g. microarray 'heat maps' and bioactivity data) as they are particularly suited to complex data sets and offer an alternative to the graphical representations included in traditional statistical software packages. The effectiveness of color-grids lies in their graphical design, which introduces a standard for customizable data representation. Currently, software applications capable of generating limited color-grid representations can be found only in advanced statistical packages or custom programs (e.g. micro-array analysis tools), often associated with steep learning curves and requiring expert knowledge.ResultsHere we describe JColorGrid, a Java library and platform independent application that renders color-grid graphics from data. The software can be used as a Java library, as a command-line application, and as a color-grid parameter interface and graphical viewer application. Data, titles, and data labels are input as tab-delimited text files or Microsoft Excel spreadsheets and the color-grid settings are specified through the graphical interface or a text configuration file. JColorGrid allows both user graphical data exploration as well as a means of automatically rendering color-grids from data as part of research pipelines.ConclusionThe program has been tested on Windows, Mac, and Linux operating systems, and the binary executables and source files are available for download at .
Highlights
Two-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions
We were inspired in part by heat maps that effectively use color as an additional dimension, a technique successfully applied to microarray data visualization
The spreadsheet and tab-delimited text formats were chosen for JColorGrid, as many scientists already manipulate data using these formats and have ready access to suitable software environments
Summary
The spreadsheet and tab-delimited text formats were chosen for JColorGrid, as many scientists already manipulate data using these formats and have ready access to suitable software environments. In the event JColorGrid reads an Excel file containing cells formatted as text, these text cells will be colored based on a set of configurable exception colors, distinct from the colors used in the color scale corresponding to the numerical data. The ability to process text data allows users to flag certain data points that require special color treatment within a larger numerical data set, a feature we term 'exceptions'. If they are present in a data set, these text exceptions are listed, along with the associated color, in an exceptions key (see 'No Data', Figure 1D). All authors contributed to the preparation of the manuscript, and have read and approved the final manuscript
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