CoV-HiPathia

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====== Pathway viewer ====== A pathway viewer has been develop in order to make easier the visualization of the comparison results. {{ :hipathia_viewer.png?600 |}} You can select the pathway to see in the //Pathways list// (**1**). You can also visualize a single subpath by clicking on its name (**3**) in the //Available subpaths// list (**2**). Subpaths depicted in blue are significantly down-regulated subpaths whereas those depicted in red are significantly up-regulated ones (p-value = 0.05). Subpaths depicted in grey are not significant. ===== Legend ===== {{ :pretty_legend.png?600 |}} 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 (only when parameter //Color nodes by differential expression// has been selected): * **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: * Subpaths which are **up-regulated** in the disease condition have their arrows colored in **red**. * Subpaths which are **down-regulated** in the disease condition have their arrows colored in **blue**. * Subpaths which are **not significative** for the test have their arrows colored in **grey**. * When an edge belongs to different subpathways which should be colored in different colors, different arrows are depicted, each one for each necessary color.