qtlcharts (version 0.16)

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
)

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.)

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.

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.

See Also

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

Examples

# NOT RUN {
library(qtl)
data(hyper)
marker <- sample(markernames(hyper), 1)
# }
# NOT RUN {
iplotPXG(hyper, marker)

# different colors
iplotPXG(hyper, marker, chartOpts=list(pointcolor=c("black", "gray")))
# }
# NOT RUN {
# }