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.