Bioinformatics Programming Using Python

Chapter 11. Structured Graphics

Bioinformatics deals with enormous amounts of data. People process visual imagery far more easily and quickly than words and numbers, so many bioinformatics websites and applications provide highly effective visualizations of complex data. Generating graphical presentations is an important aspect of bioinformatics programming. This chapter will show you how to do it.

We will look at implementations of three kinds of information displays:

• Histograms are useful for anything involving counts. They are used widely in many fields and business operations. In bioinformatics, they are frequently used to provide high-level visual overviews of quantitative distributions.

• Dot plots are also a general-purpose chart type, but in bioinformatics they have special uses for visualizing how two sequences—or a sequence and itself—are related.

• Raw data collected from laboratory devices such as sequencing machines is usually displayed as curves. The classic example is the four-colored “trace” of the data from a traditional sequencing device.

The data used for all of the examples can be found on the book’s website. In writing your own applications, you can obtain similar data via URL queries.

Introduction to Graphics Programming

Computers represent visual images in one of two ways:

Bitmaps

A bitmap is a two-dimensional arrangement of pixels, each representing the color of a “dot” at a particular location in the image.

Structured graphics

A structured image is a set of instructions ...