plot_overlaps: Plot overlaps.

In letaylor/variantBedOverlap: Calculates the overlap of variants in LD with features from BED files

Description

plot_overlaps plots the data.frame returned by get_bed_overlaps.

Usage

plot_overlaps(df, xid_solid_line = NULL, varshney_chrhmm = FALSE)

Arguments

df	Data.frame. Data.frame with at least these columns: CHROM, POS, ID, 'bed.*'. The 'bed.*' column names define y-axis labels, 'bed.*' column values define the plot colors, and the ID column values define the x-axis labels.
xid_solid_line	Character vector. A solid verticle line will be added to the plot at any x-axis value that is contained within this character vector.
varshney_chrhmm	Logical. If TRUE, the function assumes the values of the 'bed.*' columns are chromatin states from Varsheny et al 2017 (https://doi.org/10.1073/pnas.1621192114) and will format the labels to make a more polished plot.

Value

List. A list with the following elements:

plt

object from ggplot2

df

data.frame of the plot data

letaylor/variantBedOverlap documentation built on Dec. 24, 2019, 11:21 a.m.