qtl2dplotly: 2D QTL cis/trans visualization (Plotly)

In gap: Genetic Analysis Package

2D QTL cis/trans visualization (Plotly)

Description

Interactive visualization of QTL–gene relationships in 2D genomic space, separating cis and trans associations into stable Plotly traces.

Usage

qtl2dplotly(
  d,
  chrlen = gap::hg19,
  qtl.id = "SNPid:",
  qtl.prefix = "QTL:",
  qtl.gene = "Gene:",
  target.type = "Protein",
  TSS = FALSE,
  xlab = "QTL position",
  ylab = "Gene position",
  ...
)

Arguments

d	Data frame containing QTL data. Must include SNP, chromosome, position, gene mapping, and cis/trans classification.
chrlen	Chromosome length reference (default: gap::hg19).
qtl.id	Prefix for SNP identifier in tooltip.
qtl.prefix	Prefix for QTL coordinate label.
qtl.gene	Prefix for gene coordinate label.
target.type	Label for target entity type.
TSS	Logical. If TRUE, uses transcription start site.
xlab	Label for x-axis.
ylab	Label for y-axis.
...	Additional arguments passed to gap::qtl2dplot().

Details

This function wraps gap::qtl2dplot() and converts the output into an interactive Plotly scatter plot.

Unlike the original implementation, this version:

• avoids color = ~cistrans (prevents row dropping in Plotly)

• uses explicit traces for cis/trans groups

• ensures stable HTML widget rendering

• eliminates "Ignoring observations" warnings

Value

A plotly object.

Examples

## Not run: 
INF <- Sys.getenv("INF")
d <- read.csv(file.path(INF,"work","INF1.merge.cis.vs.trans"),as.is=TRUE)
r <- qtl2dplotly(d)
htmlwidgets::saveWidget(r,file="qtl2dplotly.html")
r

## End(Not run)

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