Sophisticated flavonoid pathway map based on large scale flavonoid profile datasets in Arabidopsis

How to duplicate the process in the article

Dependent software

- Cytoscape 3.2.1 (http://cytoscape.org)

- R 3.2.0 (http://www.r-project.org)

Dependent R package

- ggplot2

Reproducing Figure 2.

1. Install and run Cytoscape 3.2.1

2. Open figure3.cys with Open Session toolbar button.

Reproducing Figure 4.

1. Install R and ggplot2.

2. Run fig4.R with R. This script generates barplot png images for fig4.csv.

3. We manually created a network in fig4.cys. Then we renamed the barplot png images and mapped the images in fig4.cys. Although fig4.cys already has the custom graphics in the network, you can remap it with Cytoscape custom graphics manager.