qtl3dplotly: 3D QTL plot

In gap: Genetic Analysis Package

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",
  ...
)

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

## Not run: 
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

## End(Not run)

gap documentation built on Sept. 11, 2024, 5:36 p.m.