Local Haplotype Clustering and Visualization
Bot hap-pheno raincloud plot
Left SNP-allele plot
Left SNP-position plot
Middle MG/hap dot plot
Right intra-cluster linkage plot
Right SNP-pheno phenoplot
Hap/MG summary tables
Top metadata-hap bar plot
Clustering tree
Mode utility function
Read LD correlation matrix to tibble
Read metadata to tibble
Read phenotype data to tibble
Read VCF to tibble
crosshap: Local Haplotype Clustering and Visualization
Visualize haplotypes
Mean utility function
Pipe operator
UMAP haplotype visualization helper
Identify haplotypes from clustered SNPs
Cluster SNPs and identify haplotypes
Cluster SNPs with HDBSCAN and identify haplotypes
Calculate SNP phenotypic associations
A local haplotyping visualization toolbox to capture major patterns of co-inheritance between clusters of linked variants, whilst connecting findings to phenotypic and demographic traits across individuals. 'crosshap' enables users to explore and understand genomic variation across a trait-associated region. For an example of successful local haplotype analysis, see Marsh et al. (2022) <doi:10.1007/s00122-022-04045-8>.