Package index • qtl2ggplot

Genome Scans

Visualizing genome-wide LOD score profile curves

ggplot_scan1() autoplot(<scan1>) ggplot_scan1_internal(): Plot a genome scan
summary_scan1() summary(<scan1>): Summary of scan1 object

Coefficient Effects

Visualizing founder allele effect estimates and QTL coefficients

ggplot_coef() ggplot_coefCC() autoplot(<scan1coef>): Plot QTL effects along chromosome
ggplot_listof_scan1coef() autoplot(<listof_scan1coef>): Plot of object of class listof_scan1coeff
listof_scan1coef() summary_listof_scan1coef() summary(<listof_scan1coef>) summary_scan1coef() summary(<scan1coef>) subset_listof_scan1coef() subset(<listof_scan1coef>) `[`(<listof_scan1coef>): List of scan1coef objects

SNP Associations & Gene Annotations

High-density SNP association plots and gene locus structures

ggplot_snpasso(): Plot SNP associations
ggplot_genes() autoplot(<genes>): Plot gene locations for a genomic interval

Phenotypes, Genotypes & Peaks

Phenotype-by-genotype distributions and peak summaries

ggplot_pxg() mean_pxg(): Plot phenotype vs genotype
ggplot_onegeno(): Plot one individual's genome-wide genotypes
ggplot_peaks(): Plot QTL peak locations

Color & Pattern Utilities

Strain pattern formatting and color palette helpers

color_patterns_get(): Set up col, pattern and group for plotting.
color_patterns_set(): Set up colors for patterns or points
color_patterns_pheno(): Set up col, pattern, shape and group for plotting.
sdp_to_pattern(): Convert sdp to pattern