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  1. IGB
  2. IGBF-4076

Update Kelsey PCA axis to zoom in closer

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          GOAL: Redo the PCA's from the reference free pipeline to be zoomed in further so we can see the separation better.

          Which PCAs?
          Each tissue gets it own PCA. (2)
          each variety get its own PCA. (4)

          Symbols will be temperature.
          Colors will be time.

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              bbendick Brandon Bendickson added a comment -

              Changed the axes of all pcas to fit their respective results. Moving to review, assign back to me if further changes are needed.

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              bbendick Brandon Bendickson added a comment - Changed the axes of all pcas to fit their respective results. Moving to review, assign back to me if further changes are needed.
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              robofjoy Robert Reid added a comment -

              Better!
              I think we still need to restrain the X and Y axis to be the same coordinates.

              So that means you go choose an X-axis that best shows the separation. And then whatever you chose for X you also apply to Y-axis.
              This will squish things along the y-axis and that is OK, because it shows that relative to the X-axis, it is less important. (and that should be reflected int he PCA #'s we see too.

              In Heinz, we see that 78% of the variance is explained along the X axis. The Y only contributes 13.4%.

              Show
              robofjoy Robert Reid added a comment - Better! I think we still need to restrain the X and Y axis to be the same coordinates. So that means you go choose an X-axis that best shows the separation. And then whatever you chose for X you also apply to Y-axis. This will squish things along the y-axis and that is OK, because it shows that relative to the X-axis, it is less important. (and that should be reflected int he PCA #'s we see too. In Heinz, we see that 78% of the variance is explained along the X axis. The Y only contributes 13.4%.

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: