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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.

• In the Data card on Get data icon on the left, click Merged counts
• Scroll down and or use the search bar to find the CD19_TotalSeqB protein marker
• Click and drag the CD19_TotalSeqB marker over to the UMAP plot on the right
• Drop the CD19_TotalSeqB marker over the Color configuration option on the plot

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• Click  in the top right corner of the UMAP plot
• Lasso around the CD19 positive cells (Figure 25)
• Click  in the Filtering card on the right to Select & Filter to include the selected points

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• Select either of the UMAP plots
• Click on the Selection card on the right Select & Filter
• Click to select cluster 6 and 7
• In the Classification card on the right, Click the Classify icon then click Classify selection
• Label the cells as Doublets
• Click Save
• Click  in the Filtering card on the right to Select & Filter to exclude the selected points

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• Click  to remove the Graph-based selection rule from the Selection cardfrom Select & Filter
• Find the CD3_TotalSeqB protein marker in the biomarker table
• Click and drag CD3_TotalSeqB onto the Add rule criteria drop-down list in the Selection card Select & Filter (Figure 28)

• Set the minimum threshold to 2 in the CD3_TotalSeqB selection rule (Figure 29)

• In the Classification card on the right Classify icon, click Classify selection
• Choose Doublets from the drop-down list of cell labels
• Click Save
• Click  in the Filtering card on the right Select & Filter icon to exclude the selected points

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• Click  in the top right corner of the UMAP plot
• Lasso around the IGHD positive cells (Figure 31)
• In the Classification card Classify icon on the rightleft, click Classify selection
• Label the cells as Mature B cells 
• Click Save

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• Lasso around the IGHA1 positive cells (Figure 32)
• In the Classification card Classify icon on the rightleft, click Classify selection
• Label the cells as Activated B cells 
• Click Save

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• Click the Clear filters link in the Filtering card Select & Filter icon on the rightleft
• Select the duplicate UMAP plot (with the cell colored by marker genes)
• In the Configuration card on the Under Configure on the left, expand click the Color card Style icon and color the cells by New classifications (Figure 33)

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• Click Apply classifications in the Classification card on the right Classify icon
• Choose the Merged counts data node as input for the classification task (Figure 34)

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