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Sample PCA

Users can map the genomic data from their project using a Sample PCA plot.

PCA Image

After selecting the Sample PCA Plot module to add to their layouts, users will be presented with a settings screen to specify what is mapped. (The plot above was made using the settings shown in the image below).

PCA settings

If you do not check the "Choose specific genes" checkbox, you will be asked you to specify the following information:

  • Statistical Function (Standard Deviation, Average, or Median)
  • Sort Genes (Ascending or Descending)
  • Top # of Genes to Graph

If you click the "Choose specific genes" checkbox (as shown below), you'll be asked to select which Plot Genes you wish to add to the map. You can add more by clicking the Add Gene button or remove a gene by clicking the X beside the selected gene.

Plot Settings

If we apply these settings with the data in our project, the data is visualized in the PCA plot below.

Plot Image 2

You may also compare cohorts by checking the "Compare to Cohort" checkbox, then specifying the cohort to compare (multiple can be selected by clicking the Add Cohort button)

At the bottom left of the module, users can click View Data to see the data plotted (as shown below).

Plot Data

Style

The Style tab allows you to adjust the colors of your 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