...

The 3D UMAP plot opens in a new data viewer session (Figure 2). Each point is a different cell and they are clustered based on how similar their expression profiles are across proteins and genes. Because a graph-based clustering task was performed upstream, a biomarker table is also displayed under the plot. This table lists the proteins and genes that are most highly expressed in each graph-based cluster. The graph-based clustering found 11 clusters, so there are 11 columns in the biomarker table.

• Click and drag the 2D scatter plot icon from the Available plots card onto the New plot onto the canvas (Figure 2)
• Drop the 2D scatter plot to the right of the UMAP plot

...

• Click Merged counts to use as data for the 2D scatter plot (Figure 3)

...

• In the Selection card on the right, click Rule to In Select & Filter, click Criteria to change the selection mode
• Click the blue circle next to the Add rule drop-down menu (Figure 5)

...

• Click Merged counts to change the data source
• Choose CD3_TotalSeqB from the drop-down list (Figure 6)

...

• Click and drag the slider on the CD3D_TotalSeqB selection rule to include the CD3 positive cells (Figure 7)

...

As you move the slider up and down, the corresponding points on both plots will dynamically update. The cells with a high expression for the CD3 protein marker (a marker for T cells) are highlighted and the deselected points are dimmed (Figure 8).

...

• Click Merged counts in the Data card Get data on the left under Setup
• Click and drag CD8a_TotalSeqB onto the 2D scatter plot (Figure 9)
• Drop CD8_TotalSeqB onto the x-axis configuration option

...

The CD3 positive cells are still selected, but now you can see how they separate into CD4 and CD8 positive populations (Figure 10).

...

• Click Merged counts in the Data card on the left Get Data icon under Setup
• Search for the CD4 gene
• Click and drag CD4 onto the duplicated 2D scatter plot
• Drop the CD4 gene onto the y-axis option
• Search for the CD8A gene
• Click and drag CD8A onto the duplicated 2D scatter plot
• Drop the CD8A gene onto the x-axis option

...

• Click  in Filtering card on the right the Select & Filter tool to include the selected points
• Click  in the top right of the plot to switch back to pointer mode
• Click and drag the plot to rotate it around

...

If you need to create more space on the canvas, hide the selection panel using the Image Removedicon on the right and/or the Image Removed icon to hide the menu on the leftwords on the left using the arrow Image Added.

...

• In the Selection card on the right Select & Filter, click  to remove the CD3_TotalSeqB filtering rule
• Click the blue circle next to the Add rule dropcriteria drop-down list
• Search for Graph to search for a data source
• Select Graph-based clustering (derived from the Merged counts > PCA data nodes)
• Click the Add rule dropcriteria drop-down list and choose Graph-based to add a selection rule (Figure 20)

...