arith_mode |
Mode utility function |
build_bot_halfeyeplot |
Bot hap-pheno raincloud plot |
build_left_alleleplot |
Left SNP-allele plot |
build_left_posplot |
Left SNP-position plot |
build_mid_dotplot |
Middle MG/hap dot plot |
build_right_clusterplot |
Right intra-cluster linkage plot |
build_right_phenoplot |
Right SNP-pheno phenoplot |
build_summary_tables |
Hap/MG summary tables |
build_top_metaplot |
Top metadata-hap bar plot |
clustree_viz |
Clustering tree |
crosshap_viz |
Visualize haplotypes |
HapObject |
Example Haplotype object |
LD |
Example LD matrix |
mean_na.rm |
Mean utility function |
metadata |
Example Domestication metadata |
pheno |
Example phenotype data |
prepare_hap_umap |
UMAP haplotype visualization helper |
pseudo_haps |
Identify haplotypes from clustered SNPs |
read_LD |
Read LD correlation matrix to tibble |
read_metadata |
Read metadata to tibble |
read_pheno |
Read phenotype data to tibble |
read_vcf |
Read VCF to tibble |
run_haplotyping |
Cluster SNPs and identify haplotypes |
run_hdbscan_haplotyping |
Cluster SNPs with HDBSCAN and identify haplotypes |
tagphenos |
Calculate SNP phenotypic associations |
vcf |
Example VCF |