SingleCell - Percentage of Expressing Cells

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Contents

Overview

The view is available for all UMI SingleCell lands. In order to access it:

  • open a UMI-based Single Cell Land
  • search for a gene
  • “Select View” - scRNA-Seq Quantification section.

PercentageOfExpressingCellsSelectPlot.png

This View displays the percentage of cells expressing a gene of interest for each clusterCellType, or any other metadata of interest. This View is useful for emphasizing how many cells express your gene of interest, regardless of the detected level.

PercentageOfExpressingCellsPlot.png

View Functionalities

A. Display legend for the plotted metadata column

B.Plot Tasks

Data

Users can:

  • Change the Profile Column(s) by which the percentage of cells expressing the selected gene is displayed;
    • any Sample, Project, or CellCluster metadata column can be selected
    • more than one metadata column can be selected
  • Sort and/or Reorder Profiles
  • Choose to display or hide the groups where the selected gene is not expressed

Trellis

  • Trellis by Row Covariate
  • Remove Trellis

Customization and Properties

Users can:

  • Change chart and axis labels, names and formatting;
  • Change fill properties;
  • Flip the X and Y axes.

Export

Users can export data in text editor or Excel.


C. Filter Data

Users can filter data by

  • Sample Metadata
  • Project Metadata
  • Cell Cluster Metadata

CellClusterFilterTab.png

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

Users can select one or more bars from the plot and visualize details for:

  • the cellCluster, Sample, Project, or Clinical metadata of the selected data.
  • the expression levels of the gene of interest, for the selected CellClusters