overlay_plot: Plot overlaying eQTL and GWAS data

In myles-lewis/locuszoomr: Gene Locus Plot with Gene Annotations

Plot overlaying eQTL and GWAS data

Description

Experimental plotting function for overlaying eQTL data from GTEx on top of GWAS results. y axis shows the -log10 p-value for the GWAS result. Significant eQTL for the specified gene are overlaid using colours and symbols.

Usage

overlay_plot(
  loc,
  base_col = "black",
  alpha = 0.5,
  scheme = "RdYlBu",
  tissue = "Whole Blood",
  eqtl_gene = loc$gene,
  legend_pos = "topright",
  ...
)

Arguments

loc	Object of class 'locus' to use for plot. See locus().
base_col	Colour of points for SNPs which do not have eQTLs.
alpha	Alpha opacity for non-eQTL points
scheme	Character string specifying palette for effect size showing up/downregulation eQTL using grDevices::hcl.colors. Alternatively a vector of 6 colours.
tissue	GTex tissue in which eQTL has been measured
eqtl_gene	Gene showing eQTL effect
legend_pos	Character value specifying legend position. See legend().
...	Other arguments passed to locus_plot() for the locus plot.

Value

No return value. Produces a plot using base graphics.

myles-lewis/locuszoomr documentation built on April 16, 2024, 11:13 p.m.