SingleCell - CellMap (Expression Overlay) View

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The view is available for all SingleCell lands and it can be accessed from the “Select View” list, scRNA-Seq Quantification section.

The view displays the expression level of the selected gene, in every CellMap which passes the filtering criteria By default, there is a trellis of plots: one for each Cell Map in the Land. Some projects might have more than one CellMap, depending on the dimension reduction analysis which were applied.

Cell Map = Internal term for Dimension Reduction results; The set of individual cells used to perform a tSNE/UMAP/PCA dimension reduction analysis. Almost always a single biological sample, but sometimes will be performed on a mix of similar samples (e.g. pre- and post-treatment) to capture changes in profiles.

The default coloring of the plots is by ExpressionLevel.


When to Use this View

Use this view to explore a gene's expression pattern in the available CellMaps.

Land Data Requirements

The land must contain:

  • Metadata for Projects, Samples, CellMaps and CellClusters
  • Expression levels for the selected gene

Features of the View

A. Legend

The legend displays either

  • the coloring for the expression levels (i.e,small, medium, high)
  • the color codes for the profile column used for coloring the CellMaps

B. Chart Tasks


Users can toggle between coloring the CellMaps by Expression Level (default) or by a Profile Column.

If the toggle is set to coloring by Profile Column, the default coloring is by ClusterCellType


Users can color the CellMaps by any Metadata Column:

  • Click on Specify Profile Column
  • Select one of the columns

Customization and Properties

Users can

  • Change chart properties such as general chart properties, Symbol Properties, Color Properties
  • Flip X/Y Axis
  • Toggle between speed/quality first modes

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 data from a specific CellMap 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