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Oncoprint

Oncoprint allows users to visualize gene mutations.

Oncoprint Image

Users selecting the Oncoprint module to add to their layouts will be presented with a settings screen (shown below) to specify what is displayed.

The above image was built using data stored in the PHC for this project and the settings specified below.

Oncoprint Settings

The Oncoprint module includes a View Data button on the lower right. Clicking this opens a popup with the data displayed in the Oncoprint (as shown below).

Oncoprint Data

General

Title - Give your Oncoprint module a name. This will be displayed at the top right of the module.

Sequence Types You can check the Somatic and/or Germline checkboxes, or you can leave both unchecked.

Genes Select which Genes you wish to add to the display. You can add more by clicking the Add Gene button or remove a gene by clicking the X beside the selected gene.

Style

The Style tab allows you to adjust the colors of your bar chart. You can also load a palette for more color options.

Style

Advanced

The Advanced tab allows you to adjust the margins of your module,though this function is not commonly used.

Advanced

  1. Click Preview at the top of the module settings to view it.
  2. If everything looks good, click Apply to apply the new settings. This will NOT save the module. If you click away, you will lose this module.
  3. To save this module and its settings to the layout, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

Note

Clicking Apply will create your chart. It does not save the layout. To save the layout, you must click the Save Changes icon (found in the blue header). Navigating away from this page before clicking the icon will cause you to lose all changes since your last save.


Last update: 2021-04-20