iplotPXG | R Documentation |
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")))
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