Function reference • hypogen

Basic hamlet popgen functions Core idea of the package.
`hypogen`	hypogen: Provides Hypoplectrus PopGen Data and Functions
`geom_hypo_LG()`	Shaded LG backgrounds
`hypo_which_CHROM()`	Determining the LG from the genomic positions
`hypo_which_CHROM_s()`	Determining the LG from the genomic position
`scale_color_hypo_LG()`	Set LG color palette
`scale_fill_hypo_LG_bg()`	Set LG fill
`scale_x_hypo_LG()`	Format genome wide x axis
`theme_hypo()`	Set hypogen plot theme
`theme_hypo_anno_extra()`	Set hypogen plot theme
Data Sets and Defaults Data that comes with the pckage
`hypo_chrom_start`	Hamlet Genome Linkage Group Start Positions.
`hypo_karyotype`	Hamlet Genome Karyotype.
`hypo_clr_LGs`	Hamlet Genome Color Scheme.
`hypo_clr_lg`	Hamlet Genome LG Background Color.
Import popgen stats Functions dealing data import.
`hypo_hwe()`	Compute Hardy-Weinberg genopye frequencies
`hypo_import_genotype_freq()`	Import genotype frequencies
`hypo_import_snps()`	Import SNP based statistics
`hypo_import_windows()`	Import window based statistics
Hamlet genome geoms etc Providing hamlet genome ggplot context.
`geom_hypobg()`	Add linkage group annotation
`guide_colorbar_hypobg()`	Clone of guide_colorbar for linkage group background
`scale_hypobg_distiller()`	Scale Linkage Group background
`scale_hypobg_manual()`	Manual linkage group color scale
Zoom on genome annotation Accessing the genome annotation.
`hypo_annotation_baseplot()`	Plotting the annotation data frame
`hypo_annotation_get()`	Loading the annotation data frame

Reference