Generate enrichment analysis plots — plot

This function runs KEGG and GO enrichment analysis of peak files and generates dot plots.

plot_enrichment(
  peaklist,
  txdb = NULL,
  tss_distance = c(-3000, 3000),
  pvalueCutoff = 0.05,
  interact = FALSE,
  verbose = TRUE
)

Arguments

peaklist: A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.
txdb: A TxDb annotation object from Bioconductor.
tss_distance: A vector specifying the distance upstream and downstream around transcription start sites (TSS). The default value is c(-3000,3000); meaning peak frequency 3000bp upstream and downstream of TSS will be displayed.
pvalueCutoff: P-value cutoff, passed to compareCluster.
interact: Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.
verbose: Print messages.

Value

KEGG and GO dot plots

Examples

### Load Data ###
data("CnT_H3K27ac") # example peakfile GRanges object
data("CnR_H3K27ac") # example peakfile GRanges object 
### Create Named Peaklist ###
peaklist <- list("CnT"=CnT_H3K27ac, "CnR"=CnR_H3K27ac) 
enrich_res <- plot_enrichment(peaklist = peaklist, pvalueCutoff=1,
                              tss_distance = c(-50,50)) 
#> --- Running plot_enrichment() ---
#> 
#> Warning: >> TxDb is not specified, use 'TxDb.Hsapiens.UCSC.hg19.knownGene' by default...
#> Warning: >> TxDb is not specified, use 'TxDb.Hsapiens.UCSC.hg19.knownGene' by default...
#> + Running clusterProfiler::compareCluster for KEGG.
#> + Running clusterProfiler::compareCluster for GO.
#> plot_enrichment(): Done in 20s.