# Local Haplotype Clustering and Visualization

## Documentation for package ‘crosshap’ version 1.4.0

- DESCRIPTION file
- Package README

## Help Pages

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