Visualize Enrichment — VizEnrich • biopipen.utils

Visualize enrichment (over-representation) analysis results

Usage

VizEnrich(
  enrich,
  outprefix = NULL,
  devpars = list(res = 100),
  more_formats = c(),
  save_code = FALSE,
  ...
)

Arguments

enrich: Enrichment object from RunEnrichment
outprefix: Prefix of the output file
devpars: List of parameters to save the plot
more_formats: Additional formats to save the plot in addition to 'png'
save_code: Whether to save the code to reproduce the plot
...: Additional arguments to pass to the plot function scplotter::EnrichmentPlot

Value

A ggplot object if 'outprefix' is NULL, otherwise, save the plot to the output directory

Examples

# \donttest{
degs <- suppressWarnings(RunSeuratDEAnalysis(SeuratObject::pbmc_small, "groups", "g1", "g2"))
enrich <- RunEnrichment(degs, deg = "abs(avg_log2FC) > 1")
#> Connection changed to https://maayanlab.cloud/Enrichr/
#> Connection is Live!
#> Uploading data to Enrichr... Done.
#>   Querying KEGG_2021_Human... Done.
#> Parsing results... Done.
VizEnrich(enrich)

VizEnrich(enrich, plot_type = "dot")

VizEnrich(enrich, plot_type = "lollipop")

VizEnrich(enrich, plot_type = "network")
#> Warning: Unknown or uninitialised column: `Database`.

# VizEnrich(enrich, plot_type = "enrichmap")
# VizEnrich(enrich, plot_type = "wordcloud")
# }