eqtl_plot: Locus eQTL plot

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

Locus eQTL plot

Description

Produces a plot of eQTL data embedded in a 'locus' class object. Intended for use with set_layers().

Usage

eqtl_plot(
  loc,
  tissue = "Whole Blood",
  eqtl_gene = loc$gene,
  scheme = "RdYlBu",
  col = NA,
  pcutoff = NULL,
  xlab = NULL,
  ylab = expression("-log"[10] ~ "P"),
  cex.axis = 0.9,
  xticks = TRUE,
  border = FALSE,
  add = FALSE,
  align = TRUE,
  legend_pos = "topright",
  ...
)

Arguments

loc	Object of class 'locus' to use for plot. See locus.
tissue	GTex tissue in which eQTL has been measured
eqtl_gene	Gene showing eQTL effect
scheme	Character string specifying palette for effect size showing up/downregulation eQTL using grDevices::hcl.colors. Alternatively a vector of 6 colours.
col	Outline point colour. NA for no outlines.
pcutoff	Cut-off for p value significance. Defaults to p = 5e-08. Set to NULL to disable.
xlab	x axis title.
ylab	y axis title.
cex.axis	Specifies font size for axis numbering.
xticks	Logical whether x axis numbers and axis title are plotted.
border	Logical whether a bounding box is plotted around upper and lower plots.
add	Logical whether to add points to an existing plot or generate a new plot.
align	Logical whether set par() to align the plot.
legend_pos	Character value specifying legend position. See legend().
...	Other arguments passed to plot() for the scatter plot.

Value

No return value. Produces a scatter plot using base graphics.

See Also

locus() set_layers() scatter_plot()

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