iplotPXG: Interactive phenotype x genotype plot

Description

Creates an interactive graph of phenotypes vs genotypes at a marker.

Usage

iplotPXG(
  cross,
  marker,
  pheno.col = 1,
  chartOpts = NULL,
  fillgenoArgs = NULL,
  digits = 5
)

Value

An object of class `htmlwidget` that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

Arguments

cross: Object of class `"cross"`, see [qtl::read.cross()].
marker: Character string with marker name.
pheno.col: Phenotype column in cross object.
chartOpts: A list of options for configuring the chart. Each element must be named using the corresponding option.
fillgenoArgs: List of named arguments to pass to [qtl::fill.geno()], if needed.
digits: Round data to this number of significant digits before passing to the chart function. (Use NULL to not round.)

Details

The function [qtl::fill.geno()] is used to impute missing genotypes, with arguments passed as a list, for example `fillgenoArgs=list(method="argmax", error.prob=0.002, map.function="c-f")`.

Individual IDs (viewable when hovering over a point) are taken from the input `cross` object, using the [qtl::getid()] function in R/qtl.

By default, points are colored blue and pink according to whether the marker genotype is observed or inferred, respectively.

Examples

Run this code

library(qtl)
data(hyper)
marker <- sample(markernames(hyper), 1)
# \donttest{
iplotPXG(hyper, marker)

# different colors
iplotPXG(hyper, marker, chartOpts=list(pointcolor=c("black", "gray")))# }