Embedding

The Embedding tab shows the results of both tSNE and UMAP analyses. The Action Button enables you to toggle between the tSNE and the UMAP results.

Each analysis generates the same pair of plots.

•	One plot showing results colored by Clusters calculated in the Hierarchical Clustering. Each dot represents a cell. This plot helps visualize the distribution of the cell groups.

•

One plot showing results colored by level of gene expression. As before, each dot represents an individual cell. This plot helps to visualize the expression patterns of individual genes in the clusters. The Column Switcher enables you to navigate through a list of genes (all variable genes or list of marker genes provided by user).

•	Please refer to van der Maaten and Hinton (2008)1, van der Maaten (2014)2, and MacInnes and Healy (2018)3 for more information.

The plots for each analysis are shown below:

tSNE Plots

The tSNE plots are surfaced by default.

UMAP Results

The UMAP plots are surfaced when you click UMAP.

Actions

You can switch between tSNE and UMAP plots

You can exclude selected cells from the plots.

Use the drop-down menu to split the graphs based on one or more features.

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1

L.J.P. van der Maaten and G.E. Hinton. (2008) Visualizing High-Dimensional Data Using t-SNE. J. Machine Learning Res. 9:2579-2605.

2

L.J.P. van der Maaten. (2014) Accelerating t-SNE using Tree-Based Algorithms. J. Machine Learning Res. 15:3221-3245.

3

L. MacInnes and J. Healy. (2018) UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. arXiv:1802.03426.