ClusterMarkers¶

Markers for clusters of all or selected T cells.

This process is extended from MarkersFinder from the biopipen package.
MarkersFinder is a pipen process that wraps the Seurat::FindMarkers() function, and performs enrichment analysis for the markers found.

The enrichment analysis is done by enrichr.

Environment Variables¶

• ncores (type=int): Default: 1.
  Number of cores to use for parallel computing for some Seurat procedures.
  
  • Used in future::plan(strategy = "multicore", workers = <ncores>) to parallelize some Seurat procedures.
    
  • See also: https://satijalab.org/seurat/articles/future_vignette.html
• prefix_group (flag): Default: True.
  When neither ident-1 nor ident-2 is specified, should we prefix the group name to the section name?
  
• dbs (list): Default: ['KEGG_2021_Human', 'MSigDB_Hallmark_2020'].
  The dbs to do enrichment analysis for significant markers See below for all libraries.
  https://maayanlab.cloud/Enrichr/#libraries
• sigmarkers: Default: p_val_adj < 0.05 & avg_log2FC > 0.
  An expression passed to dplyr::filter() to filter the significant markers for enrichment analysis.
  Available variables are p_val, avg_log2FC, pct.1, pct.2 and p_val_adj. For example, "p_val_adj < 0.05 & abs(avg_log2FC) > 1" to select markers with adjusted p-value < 0.05 and absolute log2 fold change > 1.
  
• assay: The assay to use.
  
• volcano_genes (type=auto): Default: True.
  The genes to label in the volcano plot if they are significant markers.
  If True, all significant markers will be labeled. If False, no genes will be labeled. Otherwise, specify the genes to label.
  It could be either a string with comma separated genes, or a list of genes.
  
• subset: An expression to subset the cells for each case.
  
• rest (ns): Rest arguments for Seurat::FindMarkers().
  Use - to replace . in the argument name. For example, use min-pct instead of min.pct.
  This only works when use_presto is False.
  
  • <more>: See https://satijalab.org/seurat/reference/findmarkers
• dotplot (ns): Arguments for Seurat::DotPlot().
  Use - to replace . in the argument name. For example, use group-bar instead of group.bar.
  Note that object, features, and group-by are already specified by this process. So you don't need to specify them here.
  
  • maxgenes (type=int): Default: 20.
    The maximum number of genes to plot.
    
  • devpars (ns): The device parameters for the plots.
    
    • res (type=int): The resolution of the plots.
      
    • height (type=int): The height of the plots.
      
    • width (type=int): The width of the plots.
      
  • <more>: See https://satijalab.org/seurat/reference/doheatmap
• overlap_defaults (ns): The default options for overlapping analysis.
  
  • venn (ns): The options for the Venn diagram.
    Venn diagram can only be plotted for sections with no more than 4 cases.
    
    • devpars (ns): The device parameters for the plots.
      
      • res (type=int): Default: 100.
        The resolution of the plots.
        
      • height (type=int): Default: 600.
        The height of the plots.
        
      • width (type=int): Default: 1000.
        The width of the plots.
        
  • upset (ns): The options for the UpSet plot.
    
    • devpars (ns): The device parameters for the plots.
      
      • res (type=int): Default: 100.
        The resolution of the plots.
        
      • height (type=int): Default: 600.
        The height of the plots.
        
      • width (type=int): Default: 800.
        The width of the plots.
        
• overlap (json): Default: {}.
  The sections to do overlaping analysis, including Venn diagram and UpSet plot. The Venn diagram and UpSet plot will be plotted for the overlapping of significant markers between different cases.
  The keys of this option are the names of the sections. The values are a dict of options with keys venn and upset, values will be inherited from envs.overlap_defaults, recursively.
  You can set envs.overlap.<section>.venn to False/None to disable the Venn diagram for the section.
  It works when each is specified. In such a case, the sections will be the case names.
  This does not work for the cases where ident-1 is not specified. In case you want to do such analysis for those cases, you should enumerate the idents in different cases and specify them here.
  
• cache (type=auto): Default: /tmp.
  Where to cache to FindAllMarkers results.
  If True, cache to outdir of the job. If False, don't cache.
  Otherwise, specify the directory to cache to.
  Only works when use_presto is False (presto works fast enough).