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Graphing User Data
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Once a user has `uploaded their own data`_ to the Webapp, that data can be vizualized using the same graphing tools that are available when graphing TCGA and/or TARGET data.  However, the process for graphing user data is slightly different from how it is done with TCGA data

.. _uploaded their own data: http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/webapp/program_data_upload.html

Important sections on the Webapp front page
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The boxes in the figure below are links that are used to graph user data

.. image:: TopAnnotated.png


Step 1: Create a Cohort from your project
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* From the front page of the Webapp, click on Create Cohort to start the process
* Click on the *User Data* tab and select the project or study that will be the cohort
* Save as a new cohort

.. image:: CohortCreation.png

Step 2: Create a Variables Favorite
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* From the front page of the Webapp, click on *Create Variable Favorites* to start the process
* Click on the *Projects* tab to see the user supplied studies
* Select the variables that will be available to graph.  Note that if the study has a large number of selections, using the browser search function can help locate the item.
* Give the variables a name and click on the *Save as Favorite* button

.. image:: Variables_selected_genes.png


Step 3: Graph the favorites in a Workbook
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* From the front page of the Webapp, click on *Create a new Workbook*
* Under the *Source Data* heading, select the Variables and Cohorts that you wish to use in the graph.  In each case you will be brought to a page listing all of the available Variables or Cohorts.  Simply select the desired ones and then click the *Add to Workbook* button
* Under the *Analysis Type* heading, select the appropriate graph type.  This will cause a window to slide in from the right.
* Fill in the X and Y axis variables, select a variable to use for coloring and finally select the cohort to use.  

.. image:: GraphingStart.png

* Click on the *Update Plot* button to have the system gather the data and generate the plot.
* If changes need to be made to the plot, click on the *Edit Analysis Settings* link to bring back the graph dialog box. 

.. image:: GraphingGraphed.png