XGR_plot_peaks: Plot XGR peaks

In RajLabMSSM/echoplot: echoverse module: Locus plot creation for fine-mapping and colocalization studies

Plot XGR peaks

Description

Plots the distribution of annotations across a genomic region (x-axis).

Usage

XGR_plot_peaks(
  gr.lib,
  dat,
  fill_var = "Assay",
  facet_var = "Source",
  geom = "density",
  locus = NULL,
  adjust = 0.2,
  show_plot = TRUE,
  legend = TRUE,
  as_ggplot = TRUE,
  trim_xlims = FALSE
)

Arguments

gr.lib	GRanges object of annotations.
dat	Data.frame with at least the following columns: SNP SNP RSID CHR chromosome POS position
fill_var	Fill variable.
facet_var	Row facet variable.
geom	Plot type ("density", or "histogram").
locus	[Optional] Locus name.
adjust	The granularity of the peaks.
show_plot	Print the plot.
legend	A logical value indicates whether to show legend or not. Default is TRUE
as_ggplot	Return plot as ggplot2 (TRUE) or Tracks (FALSE) object.
trim_xlims	Trim the x-axis limits.

Value

ggbio track plot.

Examples

#### Import example query ####
gr.lib <- echoannot::xgr_example

#### Filter query ####
gr.filt <- echoannot::XGR_filter_sources(gr.lib = gr.lib)
gr.filt <- echoannot::XGR_filter_assays(gr.lib = gr.filt)

#### Plot query #####
XGR_track <- echoplot::XGR_plot_peaks(
    gr.lib = gr.filt,
    dat = echodata::BST1,
    fill_var = "Assay",
    facet_var = "Source")

RajLabMSSM/echoplot documentation built on Oct. 24, 2023, 2:41 a.m.