SingleCell - Gene Expression Violin Plot

From Array Suite Wiki

Jump to: navigation, search



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

The view displays the summarized expression data for the cells that pass the filter criteria, using a Violin Plot. The plot indicates the density of the data, range, median, and IQR.


When to Use this View

Use this view to explore a gene's expression pattern 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 gene

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 gene 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 gene is 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 the 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


E. X-axis data Transformation options

Not all transformations are scientifically meaningful for scRNA-seq data, which are stored as linear and by default displayed in Log2+0.1 TPM.

  • No Transformation - Visualize data with no scaling, as it is stored.
  • Log2 - Log-transform stored data; useful for separating linear-scale data such as RNA-seq. Samples with 0 value will be hidden.
  • SLog2
  • Exp2
  • NExp2
  • Log10
  • NLog10
  • Exp10
  • NExp10
  • Log
  • Exp
  • Abs
  • Log2xPlus0_1 - Log-transform stored data, with a small pseudocount so that no samples are hidden; useful for separating linear-scale data such as RNA-seq.
  • Log2xPlus0_001 - Log-transform stored data, with a small pseudocount so that no samples are hidden; useful for separating linear-scale data such as RNA-seq.
  • ArcSinh
  • Logit
  • Logit2

For technical details, see the Transformation page.