Expression visualization

Step 6 visualizes marker genes on the clustered object. Genes can come from an uploaded marker list or from the de novo marker genes detected in Step 5.

Gene sources

Use Upload file for a custom list. The file may be CSV or TSV and should contain one gene per row. A second column is optional and is used as a gene group selector.

Use Use de novo marker genes detected in Step 5 to pull genes directly from the differential-expression table. Choose the cluster and the number of top genes to visualize; genes are ranked by adjusted p-value.

Expression values

The Expression values selector controls the layer used for the clustered dot plot, feature plots, violin plots, and per-gene bundle:

  • Counts uses raw counts.

  • Normalized uses normalized expression.

  • Scaled uses scaled expression. If a selected gene was not already present in scale.data, Asc-Seurat scales the selected genes on demand for plotting.

Plots

Click Show Expression Plots to generate:

  • a clustered dot plot showing mean expression by cluster and percent of cells expressing each gene;

  • UMAP feature plots for the selected genes;

  • violin plots by cluster;

  • an optional per-gene zip bundle.

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