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• In the Graph-based filtering rule, click All to deselect all cells
• Click cluster 6 to select all cells in cluster 6
• In the Classification card on the rightUsing the Classify tool, click Classify selection
• Label the cells as Tfh cells (Figure 21)
• Click Save

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• Click  in the Filtering card on the right to Select & Filter to exclude the cluster 6/Tfh cells
• Click cluster 4 to select all cells in cluster 4
• In the Classification card on the rightthe Classify icon, click Classify selection
• Label the cells as Cytotoxic cells 
• Click Save
• Click  in the Filtering card on the right to Select & Filter to exclude the cluster 4/Cytotoxic cells

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• In the Classification card on the right Classify, click Classify selection
• Label the cells as Helper T cells 
• Click Save

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• Click the Clear filters link in the Filtering card on the right Select & Filter
• Select the duplicate UMAP plot (with the cell colored by marker genes)
• In the Configuration card Under Configure on the left, expand the Color card open Style and color the cells by New classifications (Figure 23)

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B cells

In addition to T-cells, we would expect to see B lymphocytes, at least some of which are malignant, in a MALT tumor sample. We can color the plot by expression of a B cell marker to locate these cells on the UMAP plot.

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