SingleCell - CellMap (Expression Overlay) View
From Array Suite Wiki
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
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
- Change chart properties such as general chart properties, Symbol Properties, Color Properties
- Flip X/Y Axis
- Toggle between speed/quality first modes
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