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• Introduction
  • The concept of CLC Single Cell Analysis Module
  • Contact information
  • System requirements and installation
    • System requirements
    • Installation of modules
    • Uninstalling modules
  • Licensing modules
    • Server License
  • Reference data management
    • The Reference Data Manager
  • Running tools and workflows
• Data import
  • Import Expression Matrix
  • Import Peak Count Matrix
  • Import Cell Annotations
  • Import Cell Clusters
  • Import Cell Clonotypes
  • Cell format in importers
  • Import Immune Reference Segments
    • IMSEQ
    • IMGT
    • Output from Import Immune Reference Segments
• Data export
  • Export Cell Ranger HDF5 Expression Matrix
  • Export Loom Expression Matrix
  • Export MEX Expression Matrix
  • Export TXT Expression Matrix
  • Export Peak Count Matrix
• Prepare Reads
  • Annotate Reads with Cell and UMI
    • Setting the sample name
    • Interpreting the output of Annotate Reads with Cell and UMI
• Creating a Gene Expression Matrix
  • Single Cell RNA-Seq Analysis
    • The Single Cell RNA-Seq Analysis report
    • The Single Cell RNA-Seq Analysis algorithm
  • QC for Single Cell
    • Empty droplets filter
    • Count-based and extra-chromosomal filters
    • Doublets filter
    • Interpreting the output of QC for Single Cell
    • Choosing barcodes to retain
    • The cell calling algorithm
    • The doublet calling algorithm
  • Normalize Single Cell Data
    • When is batch correction appropriate?
    • Interpreting the output of Normalize Single Cell Data
    • The Normalize Single Cell Data algorithm
• Cell Type Classification
  • Browse QIAGEN Cell Ontology
  • Predict Cell Types
  • Train Cell Type Classifier
    • Features used for training and prediction
    • Interpreting the output of Train Cell Type Classifier
    • SVMs for cell type classification
• Expression Analysis
  • Differential Expression for Single Cell
    • Interpreting the output of Differential Expression for Single Cell
    • The differential expression algorithm
  • Create Expression Plot
    • The Heat Map output of Create Expression Plot
    • The Dot Plot output of Create Expression Plot
    • The Violin Plot output of Create Expression Plot
• Velocity Analysis
  • Single Cell Velocity Analysis
    • Interpreting the output of Single Cell Velocity Analysis
    • The velocity estimation algorithm
  • Differential Velocity for Single Cell
  • Score Velocity Genes
    • Interpreting the output of Score Velocity Genes
  • Create Phase Portrait Plot
• Chromatin Accessibility
  • Single Cell ATAC-Seq Analysis
    • Interpreting the output of Single Cell ATAC-Seq Analysis
    • The report output from Single Cell ATAC-Seq Analysis
    • The Single Cell ATAC-Seq Analysis algorithm
  • Split Read Mapping By Cell
  • Differential Accessibility for Single Cell
    • The differential accessibility algorithm
• Immune Repertoire
  • Single Cell V(D)J-Seq Analysis
    • The report output from Single Cell V(D)J-Seq Analysis
    • The clonotype identification algorithm
  • Filter Cell Clonotypes
  • Combine Cell Clonotypes
  • Compare Cell Clonotypes
    • Interpreting the output of Compare Cell Clonotypes
  • Convert Clonotypes to Cell Annotations
    • Cell Annotations for TCR Cell Clonotypes
    • Cell Annotations for BCR Cell Clonotypes
  • The Cell Clonotypes element
    • Cell Clonotypes tables
    • Cell Clonotypes alignments
    • Cell Clonotypes Sankey plot
• Noise reduction through feature selection and dimensionality reduction
  • Feature selection and dimensionality reduction
    • Calculation of estimated biological variation
• Cell Annotation
  • Cluster Single Cell Data
    • The Cluster Single Cell Data algorithm
  • Create Heat Map for Cell Abundance
    • Interpreting the output of Create Heat Map for Cell Abundance
• Dimensionality reduction
  • UMAP for Single Cell
  • tSNE for Single Cell
• Utility tools
  • Combine Cell Annotations
  • Combine Cell Clusters
  • Convert Metadata to Cell Annotations
  • Add Information to Plot
  • Update to Common Sample Name
• Single cell template workflows from reads
  • Expression Analysis from Reads
    • Configuring the batch units for Expression Analysis from Reads
    • Output from Expression Analysis from Reads
  • Chromatin Accessibility Analysis from Reads
    • Configuring the batch units for Chromatin Accessibility Analysis from Reads
    • Output from Chromatin Accessibility Analysis from Reads
  • Chromatin Accessibility and Expression Analysis from Reads
    • Configuring the batch units for Chromatin Accessibility and Expression Analysis from Reads
    • Output from Chromatin Accessibility and Expression Analysis from Reads
    • Importing reads
  • Immune Repertoire Analysis from Reads (10xV(D)J)
    • Output from Immune Repertoire Analysis from Reads (10xV(D)J)
  • Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
    • Configuring the batch units for Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
    • Output from Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
• Single cell template workflows from imported data
  • Expression Analysis from Matrix
    • Output from Expression Analysis from Matrix
  • Chromatin Accessibility and Expression Analysis from Matrix
    • Output of Chromatin Accessibility and Expression Analysis from Matrix
  • Immune Repertoire and Expression Analysis from Clonotypes and Matrix
    • Output from Immune Repertoire and Expression Analysis from Clonotypes and Matrix
  • Importing data
• UMAP and tSNE plot functionality
  • Manual Annotation
  • Visualizing Different Types of Matrices
  • Create Subset
  • Extract to Table
  • Launching of Create Expression Plot
  • Launching of Create Heat Map for Cell Abundance
  • Launching of Differential Accessibility for Single Cell
  • Launching of Differential Expression for Single Cell
  • Launching of Differential Velocity for Single Cell
  • Launching of Score Velocity Genes
• Licensing requirements for the CLC Single Cell Analysis Module
  • Licensing modules on a Workbench
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Configure License Server connection
    • Download a static license on a non-networked computer
  • Licensing Server Extensions on a CLC Server
    • Download a static license on a non-networked machine
• Bibliography

The Heat Map output of Create Expression Plot

In a Heat Map each row corresponds to a gene and each column to a cell. The color in the 'th row and 'th column reflects the expression level of feature in cell (the color scale can be set in the Side Panel). The expression values used are z-score normalized for each gene. This allows the relative expression of genes with very different average expressions to be visualized in the same plot, but means that expression values cannot be compared between genes - only between cells for the same gene.

There are a number of options to change the appearance of the Heat Map. At the top of the Side Panel, you find the Heat Map group (see figure 7.2).

Figure 7.2: A heat map visualization of data from [MacParland et al., 2018].

• Lock width to window When you zoom in the Heat Map, you will per default only zoom in on the vertical level. This is because the width of the Heat Map is locked to the window. If you uncheck this option, you will zoom both vertically and horizontally.
• Lock height to window This is the corresponding option for the height. Note that if you check both options, you will not be able to zoom at all, since both the width and the height are fixed.
• Lock headers and footers This will ensure that you are always able to see the cell and feature names and the trees when you zoom in.
• Colors The expression levels are visualized using a gradient color scheme, where the right side color is used for high expression levels and the left side color is used for low expression levels. You can change the coloring by clicking the box, and you can change the relative coloring of the values by dragging the two knobs on the white slider above.

Below you find the Cells and Features groups. They contain options to show names, color legends, and, in the case of Features, trees at the left or right of the heat map. The tree options also control the Tree size, including the option of showing the full tree, no matter how much space it will use.

The Metadata group makes it possible to visualize all the information in the Cell Clusters and Cell Annotations supplied when the Heat Map was created:

• Legend font settings adjusts the label settings.
• Metadata layers Adds a color bar, colored according to the chosen metadata.

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