Integrated expression visualization

The integrated workflow uses the same visualization controls as the single-sample workflow, but the clustered object contains all samples.

Gene sources

Use Upload file for a custom CSV or TSV marker list with one gene per row and an optional second column for gene groups.

Use Use de novo marker genes detected in Step 3 to visualize genes directly from the integrated differential-expression results. When cluster markers are available, choose the cluster and the number of top genes to plot.

Expression values

The Expression values selector controls all generated plots:

• Counts uses raw counts.

• Normalized uses normalized expression.

• Scaled uses scaled expression and scales selected genes on demand if they were not already present in scale.data.

Plots

Click Show Expression Plots to generate the clustered dot plot, feature plots, violin plots, and optional per-gene zip bundle. For integrated objects, the plots should be interpreted together with the sample-colored UMAPs and sample-aware cluster tables from the clustering step.

Download controls are collapsed by default. Expand Download options to choose plot size, resolution, and file type.