iplotPXG: Interactive phenotype x genotype plot
In qtlcharts: Interactive Graphics for QTL Experiments

Description Usage Arguments Details Value See Also Examples

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

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

`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.)

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.

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.

[idotplot()], [iplot()], [iplotScanone()], [iplotMap()]

library(qtl)
data(hyper)
marker <- sample(markernames(hyper), 1)

iplotPXG(hyper, marker)

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