Create ChIPseeker annotation plot — plot_ChIPseeker

This function annotates peaks using ChIPseeker::annotatePeak. It outputs functional annotation of each peak file in a barplot.

plot_ChIPseeker_annotation(
  peaklist,
  txdb = NULL,
  tss_distance = c(-3000, 3000),
  interact = FALSE
)

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.
interact: Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

Value

ggplot barplot

Examples

### Load Data ###
data("CnT_H3K27ac") # example peakfile GRanges object
data("CnR_H3K27ac") # example peakfile GRanges object 
peaklist <- list("CnT"=CnT_H3K27ac, "CnR"=CnR_H3K27ac)
my_plot <- plot_ChIPseeker_annotation(peaklist = peaklist, 
                                      tss_distance = c(-50,50))
#> --- Running plot_ChIPseeker_annotation() ---
#> 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...
#> Done.