CellMapBrowser

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Contents

Overview

The view is available for all SingleCell lands and can be accessed from the “Select View” list, “Cell Map” section.

CellMap(DimensionReduction)Browser-ViewList .png

The view displays a plot for each Cell Map in the Land. Some projects might have more than one Cell Map, 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 ClusterCellType.

CellMap(DimensionReduction)Browser-Plot.png


When to Use this View

Use this view to get a visual representation of the Cell Clusters available on each Cell Map, and their relative sizes. The default coloring is by ClusterCellType. For additional insight into other specifics, such as TissueCategory, DiseaseState, etc., change the metadata column by which the Cell Clusters are colored.

Land Data Requirements

The land must contain Project, Sample, CellMap and CellCluster level metadata for the data included in the projects.

Features of the View

A. View legend for the plotted metadata column

B. Chart Tasks

Data

Change the metadata column by which the Cell Clusters are colored.

CellMap(DimensionReduction)Browser-DataTask.png

Customization and Properties

Users can

  • Change chart properties such as general chart properties, Symbol Properties
  • Flip X/Y Axis
  • Toggle between Quality-First and Speed-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

CellClusterFilterTab.png


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

Users can make a selection and the chart, and visualize the CellMap, Cell Cluster, Sample, Project, or Clinical details of the selected data.

CellMap(DimensionReduction)Browser-Details.png