Function reference • crosshap

Core analysis functions

Analysis and visualization functions

run_haplotyping(): Cluster SNPs and identify haplotypes

clustree_viz(): Clustering tree

crosshap_viz(): Visualize haplotypes

prepare_hap_umap(): UMAP haplotype visualization helper

Helper functions

Functions to read in and format data for haplotyping

read_LD(): Read LD correlation matrix to tibble

read_metadata(): Read metadata to tibble

read_vcf(): Read VCF to tibble

read_pheno(): Read phenotype data to tibble

Individual crosshap plots

Functions for building standalone plots that are stitched together by crosshap_viz()

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_top_metaplot(): Top metadata-hap bar plot

build_summary_tables(): Hap/MG summary tables

Example data

Example inputs for haplotyping and results for vignettes

LD: Example LD matrix

vcf: Example VCF

metadata: Example Domestication metadata

pheno: Example phenotype data

HapObject: Example Haplotype object

Internal functions

Functions called internally by crosshap to perform certain tasks

arith_mode(): Mode utility function

mean_na.rm(): Mean utility function

pseudo_haps(): Identify haplotypes from clustered SNPs

tagphenos(): Calculate SNP phenotypic associations

Deprecated functions

Functions from previous versions that are not actively tested and supported

run_hdbscan_haplotyping(): Cluster SNPs with HDBSCAN and identify haplotypes