SingleCell - Multi-Gene Expression Violin Plot

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The view is available for all SingleCell lands. It is the default view after searching for multiple genes. It can also be accessed from the “Select View” list, scRNA-Seq Quantification section.

The view displays a trellis of Violin plots - one for each gene of interest. Each plot shows the summarized expression data for the cells that pass the filter criteria, by indicating the density of the data, range, median, and IQR.


When to Use this View

Use this view to explore the expression pattern of multiple genes of interest, in cells from a given tissue and across tissues, to evaluate the gene's presence and specificity to tissues, cell types, and subtypes.

The default grouping is by ClusterCellType.

Land Data Requirements

The land must contain Project Metadata, Sample Metadata, CellCluster Metadata, and expression levels for the selected genes.

Features of the View

A. View legend for the plotted metadata column

B. Chart Tasks


Users can:

  • Change the Profile Column by which expression level for the selected genes is represented;
    • any Sample, Profile, or CellCluster metadata column can be selected
    • more than one metadata column can be selected
  • Sort and/or Reorder Profiles
  • Specify Transformation
  • Specify Mean Summarizations
  • Specify Error Summarizations
  • Choose to display or hide the groups where the selected genes are not expressed


Customization and Properties

Users can

  • Change chart properties such as general chart properties, Symbol Properties, Fill Properties
  • Flip X/Y Axis
  • Change the plot type from "Specify Profile Gallery"; for example, the data can be displayed using a BoxPlot instead of a violin plot.


Export Data

Users can export plot data in a text editor or Excel.

C. Filter Data

Users can filter data by

  • Sample Metadata
  • Project Metadata
  • Cell Cluster Metadata


D. Make a chart Selection and View Details for the selected data

Users can select one or more violins from a plot and visualize:

  • the Cell Cluster, Sample, Project, or Clinical details of the selected data.
  • the expression levels for the gene of interest, in the selected cells