Advanced plots

The Advanced Plots tool visualizes multiple genes at once from a clustered Seurat object. It can use an uploaded RDS file, the current Single Sample object, or the current Integration object.

The expression visualization tools (single sample, integrated) focus on the standard Step 6 / Step 4 workflow. The Advanced Plots tab complements those modules by plotting many marker genes in one stacked violin plot or one multi-gene dot plot.

Gene list format

Upload a CSV or TSV marker-gene file. The first column should contain gene IDs. A second column is optional and can be used as a grouping variable when organizing the gene list. The tool keeps only genes that are present in the selected Seurat object.

Use Genes to plot to include all matching genes or only the first N genes from the uploaded file. After the first plot is generated, the ordering panel lets you adjust the display order of genes and clusters before regenerating the plot.

Stacked violin plot

Stacked violin plots show the distribution of expression for several genes across clusters in a compact vertical layout. Asc-Seurat builds this plot with scCustomize::Stacked_VlnPlot.

Multi-gene dot plot

The multi-gene dot plot summarizes the same gene set by average expression and the percentage of cells expressing each gene in each cluster. Asc-Seurat builds this plot with scCustomize::DotPlot_scCustom.