TCRClusterStats¶

Statistics of TCR clusters, generated by TCRClustering.

The statistics include

• The number of cells in each cluster (cluster size)
• Sample diversity using TCR clusters instead of TCR clones
• Shared TCR clusters between samples

Environment Variables¶

• cluster_size (ns): The distribution of size of each cluster.
  
  • by: Default: Sample.
    The variables (column names) used to fill the histogram.
    Only a single column is supported.
    
  • devpars (ns): The parameters for the plotting device.
    
    • width (type=int): Default: 1000.
      The width of the device
    • height (type=int): Default: 900.
      The height of the device
    • res (type=int): Default: 100.
      The resolution of the device
  • cases (type=json): Default: {}.
    If you have multiple cases, you can use this argument to specify them. The keys will be the names of the cases. The values will be passed to the corresponding arguments above. If any of these arguments are not specified, the values in envs.cluster_size will be used. If NO cases are specified, the default case will be added, with the name DEFAULT.
    
• shared_clusters (ns): Stats about shared TCR clusters
  • numbers_on_heatmap (flag): Default: True.
    Whether to show the numbers on the heatmap.
    
  • heatmap_meta (list): Default: [].
    The columns of metadata to show on the heatmap.
    
  • cluster_rows (flag): Default: True.
    Whether to cluster the rows on the heatmap.
    
  • sample_order: The order of the samples on the heatmap.
    Either a string separated by , or a list of sample names.
    This only works for columns if cluster_rows is True.
    
  • grouping: The groups to investigate the shared clusters.
    If specified, venn diagrams will be drawn instead of heatmaps.
    In such case, numbers_on_heatmap and heatmap_meta will be ignored.
    
  • devpars (ns): The parameters for the plotting device.
    
    • width (type=int): Default: 1000.
      The width of the device
    • height (type=int): Default: 1000.
      The height of the device
    • res (type=int): Default: 100.
      The resolution of the device
  • cases (type=json): Default: {}.
    If you have multiple cases, you can use this argument to specify them. The keys will be the names of the cases. The values will be passed to the corresponding arguments above. If any of these arguments are not specified, the values in envs.shared_clusters will be used. If NO cases are specified, the default case will be added, with the name DEFAULT.
    
• sample_diversity (ns): Sample diversity using TCR clusters instead of clones.
  
  • by: The variables (column names) to group samples.
    Multiple columns should be separated by ,.
    
  • method (choice): Default: gini.
    The method to calculate diversity.
    
    • gini: The Gini coefficient.
      It measures the inequality among values of a frequency distribution (for example levels of income).
      
    • gini.simp: The Gini-Simpson index.
      It is the probability of interspecific encounter, i.e., probability that two entities represent different types.
      
    • inv.simp: Inverse Simpson index.
      It is the effective number of types that is obtained when the weighted arithmetic mean is used to quantify average proportional abundance of types in the dataset of interest.
      
    • div: true diversity, or the effective number of types.
      It refers to the number of equally abundant types needed for the average proportional abundance of the types to equal that observed in the dataset of interest where all types may not be equally abundant.
      
  • devpars (ns): The parameters for the plotting device.
    
    • width (type=int): Default: 1000.
      The width of the device
    • height (type=int): Default: 1000.
      The height of the device
    • res (type=int): Default: 100.
      The resolution of the device
  • cases (type=json): Default: {}.
    If you have multiple cases, you can use this argument to specify them. The keys will be the names of the cases. The values will be passed to the corresponding arguments above. If any of these arguments are not specified, the values in envs.sample_diversity will be used. If NO cases are specified, the default case will be added, with the name DEFAULT.
    

Examples¶

Cluster size¶

[TCRClusterStats.envs.cluster_size]
by = "Sample"

Shared clusters¶

[TCRClusterStats.envs.shared_clusters]
numbers_on_heatmap = true
heatmap_meta = ["region"]

Sample diversity¶

[TCRClusterStats.envs.sample_diversity]
method = "gini"

Compared to the sample diversity using TCR clones: