Local Haplotype Clustering and Visualization
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Documentation for package ‘crosshap’ version 1.4.0
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 |