TopExpressingGenesOfAllCells¶

Top expressing genes for clusters of all cells.

Input¶

• srtobj: The seurat object in RDS or qs/qs2 format

Output¶

• outdir: Default: {{in.srtobj | stem}}.top_expressing_genes.
  The output directory for the tables and plots

Environment Variables¶

• dbs (list): Default: ['KEGG_2021_Human', 'MSigDB_Hallmark_2020'].
  The dbs to do enrichment analysis for significant markers.
  You can use built-in dbs in enrichit, or provide your own gmt files.
  See also https://pwwang.github.io/enrichit/reference/FetchGMT.html.
  The built-in dbs include:
  
  • "BioCarta" or "BioCarta_2016"
  • "GO_Biological_Process" or "GO_Biological_Process_2025"
  • "GO_Cellular_Component" or "GO_Cellular_Component_2025"
  • "GO_Molecular_Function" or "GO_Molecular_Function_2025"
  • "KEGG", "KEGG_Human", "KEGG_2021", or "KEGG_2021_Human"
  • "Hallmark", "MSigDB_Hallmark", or "MSigDB_Hallmark_2020"
  • "Reactome", "Reactome_Pathways", or "Reactome_Pathways_2024"
  • "WikiPathways", "WikiPathways_2024", "WikiPathways_Human", or "WikiPathways_2024_Human"
• n (type=int): Default: 250.
  The number of top expressing genes to find.
  
• enrich_style (choice): Default: enrichr.
  The style of the enrichment analysis.
  The enrichment analysis will be done by EnrichIt() from enrichit.
  Two styles are available:
  
  • enrichr: enrichr style enrichment analysis (fisher's exact test will be used).
    
  • clusterprofiler: clusterProfiler style enrichment analysis (hypergeometric test will be used).
    
  • clusterProfiler: alias for clusterprofiler
• enrich_plots_defaults (ns): Default options for the plots to generate for the enrichment analysis.
  
  • plot_type: The type of the plot.
    See https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html.
    Available types are bar, dot, lollipop, network, enrichmap and wordcloud.
    
  • more_formats (type=list): Default: [].
    The extra formats to save the plot in.
    
  • save_code (flag): Default: False.
    Whether to save the code to generate the plot.
    
  • devpars (ns): The device parameters for the plots.
    
    • res (type=int): Default: 100.
      The resolution of the plots.
      
    • height (type=int): The height of the plots.
      
    • width (type=int): The width of the plots.
      
  • <more>: See https://pwwang.github.io/scplotter/reference/EnrichmentPlot.htmll.
    
• enrich_plots (type=json): Default: {'Bar Plot': Diot({'plot_type': 'bar', 'ncol': 1, 'top_term': 10})}.
  Cases of the plots to generate for the enrichment analysis.
  The keys are the names of the cases and the values are the dicts inherited from enrich_plots_defaults.
  The cases under envs.cases can inherit this options.
  
• subset: An expression to subset the cells for each case.
  

SeeAlso¶

• TopExpressingGenes
• ClusterMarkers for examples of enrichment plots