Uniform Manifold Approximation and Projection (UMAP)

Running UMAP analysis on Pluto to explore your data!

Uniform Manifold Approximation and Projection (UMAP) is another common non-linear dimensionality reduction method that is similar to t-SNE but preserves the local and global structure of the data. This allows for resolving more subtle differences between clustered groups and is more reproducible.

Set Up Your Analysis

  1. Navigate to your experiment and click on the + Analysis button on the right of the screen
  2. Scroll down on the sidebar and select UMAP under "Dimensionality Reduction"
  3. Hit the Next button to generate analysis parameters. Here, you can select which samples you'd like to include or exclude in your analysis if applicable.
  4. Then hit "Run Analysis"

UMAP Parameters

Customize Your Plot
  1. Use the plot tab to customize your plots by clicking the three dots on the top right of your newly generated plot and selecting "Edit"
  2. Here, you can select what projections you want on your axes, the variable to group points by and your color scheme.
  3. Select "View Changes" to apply modifications to your plot.