pathway_viewer
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pathway_viewer [2015/12/21 17:43] mhidalgo |
pathway_viewer [2020/04/03 20:18] (current) |
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| ====== Pathway viewer ====== | ====== Pathway viewer ====== | ||
| - | A pathway viewer has been develop in order to make easier the visualization of the comparison results. | + | A pathway viewer has been developed in order to make easier the visualization of the comparison results. |
| {{ :hipathia_viewer.png?600 |}} | {{ :hipathia_viewer.png?600 |}} | ||
| - | You can select the pathway to see in the //Pathways list// (**1**). | + | You can select the pathway to see in the //Categories// 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. | + | 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 ===== | ===== Legend ===== | ||
| - | {{ :pretty_legend.png?600 |}} | + | {{ :pretty_legend.png |}} |
| The information summarized in the pathway viewer includes: | The information summarized in the pathway viewer includes: | ||
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| * **Rectangles** are cellular functions. | * **Rectangles** are cellular functions. | ||
| - | Node's color (only when parameter //Color nodes by differential expression// has been selected): | + | Node's color: |
| * **Blue** for down-regulated genes, **red** for up-regulated genes and **grey** for not significant genes. | * **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. | * The intensity of the color depends on the significance of the differential expression. | ||
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| Edge's color: | Edge's color: | ||
| - | * Subpaths which are **up-regulated** in the disease condition have their arrows colored in **red**. | + | * Circuits 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**. | + | * Circuits 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**. | + | * Circuits which are **not significant** 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. | + | * **When an edge belongs to different circuits which should be colored in different colors, different arrows are depicted, each one for each necessary color.** |
pathway_viewer.1450719818.txt.gz · Last modified: 2020/04/03 20:17 (external edit)
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