====== Pathway viewer ======

A pathway viewer has been developed in order to make easier the visualization of the comparison results.

{{ :hipathia_viewer.png?600 |}}

You can select the pathway to see in the //Categories// list (**1**).
You can also visualize a single circuit by clicking on its name (**3**) in the //Circuits// list (**2**). Circuits depicted in blue are significantly down-regulated circuits whereas those depicted in red are significantly up-regulated ones (p-value = 0.05). Circuits depicted in grey are not significant.

===== Legend =====


{{ :pretty_legend.png |}}

The information summarized in the pathway viewer includes:

Node's shape:
  * **Ellipses** correspond to genes.
  * **Circles** represent metabolites.
  * **Rectangles** are cellular functions.

Node's color:
  * **Blue** for down-regulated genes, **red** for up-regulated genes and **grey** for not significant genes.
  * The intensity of the color depends on the significance of the differential expression.

Edge's shape: Edges represent either activations or inhibitions.
  * **Activations** are represented by classic arrows.
  * **Inhibitions** are represented by T arrows.

Edge's color:
  * Circuits which are **up-regulated** in the disease condition have their arrows colored in **red**.
  * Circuits which are **down-regulated** in the disease condition have their arrows colored in **blue**. 
  * Circuits which are **not significant** for the test have their arrows colored in **grey**. 
  * **When an edge belongs to different circuits which should be colored in different colors, different arrows are depicted, each one for each necessary color.**