xQTLvisual_locusZoom: Locuszoom plot for visualizing regional signals relative to...

In dingruofan/xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Locuszoom plot for visualizing regional signals relative to genomic position with summary statistics data

Description

This function is rebuilt from locuscompare.R (https://github.com/boxiangliu/locuscomparer/blob/master/R/locuscompare.R).

Usage

xQTLvisual_locusZoom(
  DF,
  highlightSnp = "",
  population = "EUR",
  posRange = "",
  legend = TRUE,
  ylim = NULL,
  legend_position = c("topright", "bottomright", "topleft"),
  point_color = NULL,
  axis_text_size = 1.3,
  axis_title_size = 1.3,
  title_size = 1.4,
  xlab_text = "",
  ylab_text = "",
  title_text = "",
  snpLD = NULL
)

Arguments

DF	A data.frame or a data.table object. Four columns are required (arbitrary column names is supported): ⁠Col 1⁠. "snps" (character), , using an rsID (e.g. "rs11966562"); ⁠Col 2⁠. "chromosome" (character), one of the chromosome from chr1-chr22; ⁠Col 3⁠. "postion" (integer), genome position of snp. ⁠Col 4⁠. "P-value" (numeric).
highlightSnp	Default is the snp that with lowest p-value.
population	One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.
posRange	Genome range that you want to visualize (e.g. "chr6:3e7-7e7"). Default is the region that covers all snps.
legend	(boolean, optional) Should the legend be shown? Default: TRUE.
ylim	set the minimum and maximum values for the y-axis. By default, the function will automatically determine the y-axis limits based on the data being plotted.
legend_position	(character, optional) Either 'bottomright','topright', or 'topleft'. Default: 'bottomright'.
point_color	(character, optional) Customized color vectors (5 kinds of colors).
axis_text_size	(numberic) text size of the axis labels
axis_title_size	(numberic) text size of the axis title
title_size	(numberic) text size of the title of the plot
xlab_text	(character) Lable for x-axis
ylab_text	(character) Lable for x-axis
title_text	(character) Title of the plot
snpLD	A data.frame of LD matirx. Default is null.

Value

A list containing data.table and ggplot object.

Examples

library(data.table)
# For GWAS dataset:
gwasDF <- fread("https://gitee.com/stronghoney/exampleData/raw/master/gwasChr6Sub4.txt")
xQTLvisual_locusZoom(gwasDF)
# Zoom in:
xQTLvisual_locusZoom(gwasDF, posRange="chr6:4.7e7-4.8e7", population ="EUR")

# For eQTL of a gene of interest (time-consuming):
eqtlAsso <- xQTLdownload_eqtlAllAsso("RP11-385F7.1", tissueLabel = "Brain - Cortex",
                                     withB37VariantId=FALSE)
xQTLvisual_locusZoom(eqtlAsso[,c("snpId", "chrom", "pos", "pValue")], highlightSnp="rs4711878" )
# Zoom in:
xQTLvisual_locusZoom(eqtlAsso[,c("snpId", "chrom", "pos", "pValue")], highlightSnp="rs4711878",
                     posRange="chr6:47.3e6-47.9e6")

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.