3D QTL plot (cis/trans genomic visualization)

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().

Value

A plotly 3D scatter object.

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

Examples

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