TopExpressingGenes

TopExpressingGenes¶

Top expressing genes for clusters of all or selected T/B cells.

This process finds the top expressing genes of clusters of T/B cells, and also performs the enrichment analysis against the genes.

The enrichment analysis is done by enrichr.

Note

There are other environment variables also available. However, they should not be used in this process. Other environment variables are used for more complicated cases for investigating top genes (See biopipen.ns.scrna.TopExpressingGenes for more details).

If you are using pipen-board to run the pipeline (see here and here), you may see the other environment variables of this process are hidden and readonly.

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 See below for all libraries.
https://maayanlab.cloud/Enrichr/#libraries
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.