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2D QTL cis/trans visualization (Plotly)

Source: R/qtl2dplotly.R
qtl2dplotly.Rd

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().

Value

A plotly object.

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

Examples

if (FALSE) { # \dontrun{
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
} # }