xQTLvisual_locusCombine: Generate a combined figure including locusZoom and...

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

Generate a combined figure including locusZoom and locuscompare plot

Description

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

Usage

xQTLvisual_locusCombine(
  gwasEqtldata,
  posRange = "",
  population = "EUR",
  highlightSnp = "",
  legend_position = "bottomright",
  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

gwasEqtldata	A data.frame or a data.table that including signals from both GWAS and eQTL. Five 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) of GWAS signals. ⁠Col 5⁠. "P-value" (numeric) of eQTL signals.
posRange	Genome range that you want to visualize (e.g. "chr6:3e7-7e7"). Default is the region that covers all snps.
population	One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.
highlightSnp	Default is the snp that with lowest p-value.
legend_position	(string, 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 object of LD matrix. Default is null.

Value

A ggplot object.

Examples

# load data:
u1 <-"http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwas/AD/gwasEqtldata.txt"
gwasEqtldata <- data.table::fread(u1)
xQTLvisual_locusCombine(gwasEqtldata, highlightSnp="rs13120565")

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