3D QTL plot — qtl3dplotly • gap

3D QTL 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 in qtl2d() format.
chrlen: Lengths of chromosomes for specific build: hg18, hg19, hg38.
zmax: Maximum value (e.g., -log10p) to truncate, above which they would be set to this value.
qtl.id: QTL id.
qtl.prefix: QTL prefix.
qtl.gene: QTL target gene.
target.type: Type of target, e.g., protein.
TSS: to use TSS when TRUE.
xlab: X-axis title.
ylab: Y-axis title.
...: Additional arguments, e.g., to qtl2dplot().

Value

A plotly figure.

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) %>%
     mutate(log10p=-log10p)
r <- qtl3dplotly(d,zmax=300)
htmlwidgets::saveWidget(r,file=file.path(INF,"INF1.qtl3dplotly.html"))
r
} # }