Help:DataVisualizationInCytoscape

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'''UNDER CONSTRUCTION'''
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'''This tutorial has been replaced by the [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title WikiPathways App Tutorial].'''
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This tutorial describes how to visualize experimental data on WikiPathways in Cytoscape. After importing the data, it is mapped to standard identifiers using BridgeDb. A visual style is created, and the data is visualized on pathways imported from WikiPathways.  
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= Installation =
= Installation =
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=== Cytoscape ===
=== Cytoscape ===
* Download Cytoscape here: http://www.cytoscape.org/.
* Download Cytoscape here: http://www.cytoscape.org/.
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* In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''.
* In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''.
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[[image:AppManager.png|left|]]<br clear="all" />
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[[image:AppManager.png|650px|left|]]<br clear="all" />
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* In the search field, type ''WikiPathways'' to search for the WikiPathways app. In the search results, select the WikiPathways app and click '''Install'''.
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* In the search field, type ''WikiPathways'' to search for the WikiPathways app. Select the WikiPathways app from the results and click '''Install'''.
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* Next, find and install the BridgeDb app in the same way. When the installation is complete, click '''Close''' to exit the '''App Manager'''.
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* When the installation is complete, click '''Close''' to exit the '''App Manager'''.
Alternatively, Cytoscape apps can be installed directly from the Cytoscape App Store. If Cytoscape is open on your computer, you can click '''Install''' on the relevant app page, and the app will install.  
Alternatively, Cytoscape apps can be installed directly from the Cytoscape App Store. If Cytoscape is open on your computer, you can click '''Install''' on the relevant app page, and the app will install.  
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[http://apps.cytoscape.org/apps/wikipathways WikiPathways app]
[http://apps.cytoscape.org/apps/wikipathways WikiPathways app]
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[http://apps.cytoscape.org/apps/bridgedb BridgeDb app]
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= Pathway import and mapping =
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= Data import and mapping =
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=== Import pathways from WikiPathways ===
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=== Download the data ===
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Based on over-representation analysis, two pathways have been identified as significant for this dataset. To start, we will open these pathways.
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For this tutorial, we will use an example dataset describing intestinal changes in response to fasting. The data is in the form of a text file.  
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The experimental data for this tutorial can be found here: [http://opentutorials.cgl.ucsf.edu/images/f/f7/Starvation_dataset_trans.txt Starvation_dataset_trans.txt].
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* Locate the search field at the top of the Network Panel and choose WikiPathways from the pulldown options.
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* Type in ''Electron Transport'' and hit '''Enter''' or click the icon to search.
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* In the results dialog, check the  box for '''Only''' and select '''Mus musculus''' in the species drop-down.  
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* In the pathway results, select the Electron Transport Chain and either double-click on the entry to open, or click on the '''Import as Pathway''' button at the bottom right. Once opened, the pathway should look like this:
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=== Open pathways ===
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[[image:WPSearchResults.png|900px|left|]]<br clear="all" />
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Based on over-representation analysis, 4 pathways have been identified as significant for this dataset. To start, we will open these pathways.
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Once the pathway opens in Cytoscape, it should look like this:
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* Go to '''File > Import > Network > Public Databases...'''. In the '''Data Source''' drop-down, select WikiPathways.
 
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[[image:ImportNetworkDatabase.png|left|]]<br clear="all" />
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[[image:ElectronTransport.png|1100px|left|]]<br clear="all" />
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* Check the  box for '''Only''' and select '''Mus musculus''' in the species drop-down.
 
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* In the search field, type in ''Electron Transport Chain''. Click '''Enter''' to search.
 
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[[image:WPSearchResults.png|left|]]<br clear="all" />
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* Repeat the steps above to search for ''Proteasome'' and import the '''Proteasome degradation''' pathway.
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* You should now have both pathways open in Cytoscape:
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* In the pathway results, select the Electron Transport Chain and either double-click on the entry to open, or click ont he '''Import as Pathway''' button at the bottom right. Once opened, the pathway should look like this:
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[[image:PathwaysInCytoscape.png|1100px|left|]]<br clear="all" />
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[[image:ElectronTransport.png|left|]]<br clear="all" />
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=== Identifier Mapping ===
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In the Table Panel you can see that the gene identifiers in these pathways from Ensembl. It turns out that the experimental data we will be using in this example is also annotated with Ensembl identifiers. But this is not always the case! Fortunately, it is very easy to get a new column of identifiers in any of the major types.  In this example, we will go ahead and add a column of Entrez Gene IDs to demonstrate this functionality.
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* Repeat the steps above to import the following three additional pathways: '''Oxidative phosphorylation''', '''Proteasome degradation''' and '''Urea cycle and metabolism of amino groups'''.
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* In the Table Panel, right click on the column header '''XrefId''' which contains the identifiers for the data nodes.
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* You should now have all 4 pathways open in Cytoscape:
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* Choose '''map column''' to bring up the ID Mapping dialog
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* Select the following:
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** Species: '''Mouse'''
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** Map from: '''Ensembl'''
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** To: '''Entrez'''
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* Then click '''OK'''
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* Now you have a new column of Entrez Gene IDs (all the way to the right)
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[[image:PathwaysInCytoscape.png|left|]]<br clear="all" />
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'''Note that the WikiPathways app automatically adds Ensembl identifiers to pathways upon import. This means that manually annotating the pathway is only necessary if the data is annotated with a system other than Ensembl.'''
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=== Identifier mapping with BridgeDb ===
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= Data import =
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Since the data is annotated with Ensembl identifiers and the pathways have a mix of identifiers, the pathways need to be mapped to Ensembl before the data can be visualized. The BridgeDb app does exactly this, given a mapping file. Before performing the mapping, we have to import the appropriate mapping file to BridegDb.
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=== Download data ===
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For this tutorial, we will use an example dataset describing intestinal changes in response to fasting in mice. The data gene expression array data, and is in the form of a text file.  
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* Open the BridgeDb app under '''Apps > BridegDb > Manage ID Mapping Resources'''.
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The experimental data for this tutorial can be found here: [http://opentutorials.cgl.ucsf.edu/images/f/f7/Starvation_dataset_trans.txt Starvation_dataset_trans.txt].
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[[Image:BridegDb_Resources.png|left|]]<br clear="all" />
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BridgeDb works with mapping information from various sources. For example, y ou can either download a database [http://www.pathvisio.org/downloads/download-bridgedbs/ here], and after extracting it you can select it under '''Databases''' in the '''ID Mapping Resouces Configuration''' interface. You can also supply a local or remote mapping file.
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Source: [http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-361 Sokolovic et al. BMC Genomics. 2007 Oct 9;8:361]
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For this tutorial, we will use Web Services for the mappings.
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* Click on the '''Web Services''' entry in the list of ID mapping sources.
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=== Import data to Cytoscape ===
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* In the '''Webservice-based ID Mapping Resources Configuration''' interface, select '''BridegDb web service''' in the drop-down.
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* To import the experimental data, select '''File > Import > Table from File...'''. Select the ''starvation_dataset_trans.txt'' file and click '''Open'''.
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* Under '''Where to Import Table Data''', choose '''To selected networks only'''.
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* To select both pathways, click the '''Select All''' button.
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* Under '''Key Column for Networks''', select '''XrefId''' (the column with Ensembl IDs).
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* In the '''Preview''' section, click the expand symbol at the top of the '''ensid''' column. This will open an interface where you can define the details of the column, such as data type etc.
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* For the purposes of this tutorial, click the key symbol. This defines the '''ensid''' column as being the key column, which will be used to link the data to the pathways.
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[[Image:BridgeDb_webservice.png|left|]]<br clear="all" />
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[[image:DataImport.png|600px|left|]]<br clear="all" />
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* In the '''Base URL of BridgeDb web service''' drop-down, select the entry for mouse. Click '''OK''' to continue.
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* Click '''OK''' to import the data.
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You will see a listing of supported ID systems. We are now ready to perform the mapping.
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= Data visualization on pathways =
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[[Image:BridgeDb_Config.png|left|]]<br clear="all" />
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The data and pathways are now both imported and linked and we can visualize the data on the pathways. For this tutorial, we will create a color scheme for all significant nodes, based on ANOVA values for a comparison across three experimental groups.
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* Close the '''ID Mapping Source Configuration''' interface.
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* In the '''Control Panel''' on the left side of Cytoscape, select the '''Style''' tab.
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* In the list of '''Properties''' click on the triangle next to '''Fill Color''' to expand.
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* Click on '''Fill Color''' next to Column. In the drop-down, select '''ANOVA''' to select the ANOVA column from the data.
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* Under '''MappingType''', select '''Continous Mapping'''.  
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We are now ready to map the identifiers from the pathways to Ensembl. BridgeDb works best when you know the type of identifier to map from (Source).
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[[image:ContinousDefault.png|left|]]<br clear="all" />
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* To find out which identifier type(s) is used in your pathway, first select all nodes on the pathway by clicking and dragging to select the entire pathway. Selected nodes will turn yellow.
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* Immediately below the network view in Cytoscape is the '''Table Panel'''. Expand the table either by clicking dragging on the table border, or by click on the '''Float Window''' icon on the right end of the Table Panel border.
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* The identifier types for data nodes are listed in the '''XrefDatasource''' column. The 4 pathways in this tutorial are annotated with a mix of Entrez Gene, MGI and Ensembl identifiers.
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[[Image:DataNodeTable.png|left|]]<br clear="all" />
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* Double-click on the default color continuum to customize it.
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* Set the min/max values by clicking the '''Set Min and Max...''' button. Set Min to 0 and Max to 0.05.
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* Set the colors for both min and max by double-clicking on the small triangles and choosing a shade of green.
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* For the large right-most triangle, set the color to a pale gray color.
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* With one of the networks selected, go to '''Apps > BridegDb > Map Identifiers'''.  
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You now have a color scheme where nodes with an ANOVA value of 0.05 or below is colored green, and all other measured nodes are colored gray. Nodes that are not found will simply be white.
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* In the BridgeDb interface, open the drop-down under '''Source ID Type(s)''', and select Ensembl, Entrez Gene and MGI in the list of identifier types.
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=== Data import ===
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[[image:PathwayViz.png|left|]]<br clear="all" />
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* To import the experimental data, select '''File > Import > Table > File...'''. Select the ''starvation_dataset_trans.txt'' file and click '''Open'''.
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* Select the pathway collection created earlier to import the data to......
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* Select the appropriate key column......
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[[image:DataImport.png|left|]]<br clear="all" />
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=== Export visualizations ===
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Any pathway or network visualization in Cytoscape can be exported into a number of graphical file formats, which can easily be included in publications and websites. File formats supported for export are PNG, JPEG, PDF, PostScript and SVG.
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= Viewing data on pathways =
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* To export the pathway visualization, select '''File > Export > Network View as Graphics...'''
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* Select the export file format, and designate a location name filename for the export.
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=== Open WikiPathways in Cytoscape ===
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[[image:ExportPathway.png|left|]]<br clear="all" />
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=== Visual Styles ===
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-->

Current revision

This tutorial has been replaced by the WikiPathways App Tutorial.

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