plot_cistrans: cis-trans plot for eQTL results

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

cis-trans plot for eQTL results

Description

Scatterplot of gene location vs QTL location to display eQTL/pQTL results

Usage

plot_cistrans(
  peaks,
  map,
  pheno_pos,
  gap = 0,
  cis_window = 1,
  pch = 21,
  col = "slateblue",
  bg = "slateblue",
  cex = 0.8,
  pch_cis = 21,
  col_cis = "violetred",
  bg_cis = "violetred",
  cex_cis = 0.8,
  pty = "s",
  bgcolor = "gray90",
  altbgcolor = "gray80",
  ...
)

Arguments

peaks	Data frame of QTL results, as output by find_peaks() Should contain columns lodcolumn, chr, and pos.
map	Marker map, as a list of chromosomes, each being a vector of positions; used to get chromosome names and start/end
pheno_pos	Data frame with chromosome, position, and name of the phenotypes in peaks. Should contain columns pheno, chr, and pos.
gap	Gap between chromosomes in the plot
cis_window	Window size that defines cis-QTL (on same chromosome, and position of gene within this distance of QTL position)
pch	Point type for "trans" points
col	Point color for "trans" points
bg	Background color for "trans" points
cex	Character expansion size for "trans" points
pch_cis	Point type for "cis" points
col_cis	Point color for "cis" points
bg_cis	Background color for "cis" points
cex_cis	Character expansion size for "cis" points
pty	Plot type; the default "s" forces a square plot; use "m" to use the maximal plotting region.
bgcolor	Background color for chromosome rectangles
altbgcolor	Alternate background color for chromosome rectangles
...	Additional graphics arguments passed to graphics::points()

Value

Invisibly returns a data frame with peaks merged with pheno_pos, with an additional column cis that indicates which QTL appear to be cis (vs trans).

See Also

plot_scan1(), find_peaks(), plot_lodpeaks()

Examples

## Not run: 
# download example pQTL results (from Keele et al. 2026, https://doi.org/10.1016/j.xgen.2025.101069)
# contains qtl, map, and pheno_pos
url <- "https://kbroman.org/qtl2/assets/sampledata/pqtl_data.RData"
tempfile <- file.path(tempdir(), basename(url))
download.file(url, tempfile)
load(tempfile)
unlink(tempfile)

plot_cistrans(qtl, map, pheno_pos, cis_window=5)

## End(Not run)

qtl2 documentation built on July 6, 2026, 5:11 p.m.