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- Click the Merged counts data node
- Click Exploratory analysis in the toolbox
- Click Graph-based clustering
- Click Gene Expression for Include features where "Feature type" is
- Click Configure to access the advanced settings
- Set Number of principal components to 15
- Click Apply
- Click Finish to run (Figure 17)
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Once Graph-based clustering has finished running and produced a Clustering result data node, we can visualize the results using UMAP or t-SNE.
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Both are dimensional reduction techniques that group cells with similar expression into visible clusters.
- Click the Clustering result data node
- Click Exploratory analysis in the toolbox
- Click UMAP
- Click Gene Expression for Include features where "Feature type" is
- Click Configure to access the advanced settings
- Set Number of principal components to 15
- Click Apply
- Click Finish to run (Figure 18)
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The Analyses tab now includes a UMAP task node (Figure 18).
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- Double-click the UMAP task node to open the task report
The UMAP task report includes a scatter plot with the clustering results coloring the points (Figure 19).
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