Local Haplotype Clustering and Visualization


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Documentation for package ‘crosshap’ version 1.2.2

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