gap (version 1.6)

qtl3dplotly: 3D QTL plot

Description

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",
  ...
)

Value

A plotly figure.

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().

Examples

if (FALSE) {
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
}