PlotRegion • RNAPeaks

Overview

PlotRegion() renders all genes whose features overlap a specified genomic window, stacking each gene’s transcript structure and overlapping RBP peaks vertically. It is useful for visualizing binding patterns across a locus or comparing multiple genes in a region simultaneously.

library(RNAPeaks)
data(gtf_human)

Basic usage

result <- PlotRegion(
    bed    = sample_bed,
    gtf    = gtf_human,
    Chr    = "12",
    Start  = 56000000,
    End    = 56050000,
    Strand = "+"
)
result$plot

Focusing on a single gene within a region

Supply geneID to include only one gene while still using the coordinate window for peak filtering:

PlotRegion(
    bed    = sample_bed,
    gtf    = gtf_human,
    Chr    = "12",
    Start  = 56000000,
    End    = 56050000,
    Strand = "+",
    geneID = "GAPDH"
)

Saving output

result <- PlotRegion(
    bed                 = sample_bed,
    gtf                 = gtf_human,
    Chr                 = "12",
    Start               = 56000000,
    End                 = 56050000,
    Strand              = "+",
    RNA_Peaks_File_Path = "figures/region_peaks.pdf",
    Bed_File_Path       = "data/region_peaks.csv"
)

# Suppress file output
PlotRegion(
    bed                 = sample_bed,
    gtf                 = gtf_human,
    Chr                 = "12",
    Start               = 56000000,
    End                 = 56050000,
    Strand              = "+",
    RNA_Peaks_File_Path = NULL,
    Bed_File_Path       = NULL
)