pxg.plot {DOQTL} | R Documentation

## Phenotype by genotype plot at a single marker.

### Description

This function plots the phenotype versus the most probable genotype at a single marker.

### Usage

      pxg.plot(pheno, pheno.col, probs, snp.id, snps, legend = TRUE, sex = NA, covar, ...)

### Arguments

`pheno` | Data.frame containing the phenotype data with samples in rows and phenotypes in columns. Sample IDs in rownames and phenotype names in colnames.
`pheno.col` | Numeric or character vector: Either a vector of number that indicate columns to use or a set of column names in pheno.
`probs` | 3D numeric array, containing the founder haplotype contributions or genotype probabilities. The sample IDs, founder letter codes and markers IDs must be in dimnames.
`snp.id` | Character string containing the marker to plot at. Must be in SNPs and dimnames(probs)[[3]].
`snps` | Data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.
`legend` | Boolean that is true if a legend explaining the founder letter codes should be plotted.
`sex` | Character that is either FALSE or M, indicating sex. This is used only when the SNP ID is on the X chromosome and all of the samples are male. In this case, there are only 8 genotype states.
`covar` | Vector of categories for each sample (i.e. diet, treatement, etc.) which will be plotted as different symbols. Optional.
`...` | Additional arguments passed along to plot.

### Details

The most probable genotype is inferred from the eight founder allelic contributions at the marker. If a founder has a value > 0.75, it is assumed to be homozygous.

### Value

Creates a plot with the phenotype on the y-axis and the 36 DO genotypes on the x-axis.

### Author(s)

Daniel Gatti

### See Also

`plot.doqtl`, `coefplot`

### Examples

      ## Not run:  pxg.plot(pheno, pheno.col, founder.probs, snp.id, snps)

[Package DOQTL version 1.19.0 Index]