qtl3dplotly: 3D QTL plot (cis/trans genomic visualization)

In gap: Genetic Analysis Package

3D QTL plot (cis/trans genomic visualization)

Description

Interactive 3D visualization of QTL–gene relationships using a scatter3D plot.

Usage

qtl3dplotly(
  d,
  chrlen = gap::hg19,
  zmax = 300,
  qtl.id = "SNPid:",
  qtl.prefix = "QTL:",
  qtl.gene = "Gene:",
  target.type = "Protein",
  TSS = FALSE,
  xlab = "QTL position",
  ylab = "Gene position",
  ...
)

Arguments

d	Data frame in qtl2dplot()-compatible format.
chrlen	Chromosome lengths (e.g. gap::hg19, hg38).
zmax	Maximum value for z-axis truncation.
qtl.id	Prefix for SNP identifier.
qtl.prefix	Prefix for QTL coordinate label.
qtl.gene	Prefix for gene coordinate label.
target.type	Label for target entity type.
TSS	Logical; use transcription start site if TRUE.
xlab	X-axis label.
ylab	Y-axis label.
...	Additional arguments passed to qtl2dplot().

Details

This function extends gap::qtl2dplot() into a 3D representation by adding a z-axis (typically \-log10(p) or similar association strength).

Features:

• caps extreme values at zmax

• colors cis/trans associations

• provides interactive hover labels

Value

A plotly 3D scatter object.

Examples

## Not run: 
suppressMessages(library(dplyr))
INF <- Sys.getenv("INF")
d <- read.csv(
  file.path(INF, "work", "INF1.merge.cis.vs.trans"),
  as.is = TRUE
) %>%
  dplyr::mutate(log10p = -log10p)
r <- qtl3dplotly(d, zmax = 300)
htmlwidgets::saveWidget(r, file = "qtl3dplotly.html")
r

## End(Not run)

gap documentation built on Oct. 27, 2026, 1:07 a.m.