Arabidopsis eFP Viewer

Arabidopsis eFP Viewer

Arabidopsis eFP Viewer

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The Arabidopsis eFP browser is a data visualization tool for exploring which parts of a plant any gene of interest may be expressed in, and to what degree.

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Based on the original eFP browsers Nicholas Provart created for, this new implementation was written in Processing. This version includes the following upgrades:

  • a vectorized image instead of bitmap (much sharper)
  • the ability to load expression patterns for up to 40 genes instead of just one at a time
  • an abbreviated heat map for quick recognition of similar expression patterns
  • multiple color modes
  • real time toggling between absolute/relative
  • threshold and data masking options
  • and general speed improvements since it runs in a web browser instead of on the server.

I built three versions: one for Arabidopsis thaliana (thale cress), one for Solanum lycopersicum (tomato), and one for Solanum tuberosum (potato). Hans Yu and Jim Fan rewrote the program with JavaScript so it can be included in my dissertation project, ePlant.

The image above was created with ePlant. I decided to remove the black outlines around all the leafs in light of Tufte’s advice to remove all non-data ink.

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