This package is considered a duplicate. The official version of this package is found at:https://jacobimarsh.r-universe.dev/crosshap

Package: crosshap 1.4.0

Jacob Marsh

crosshap: Local Haplotype Clustering and Visualization

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>.

Authors:Jacob Marsh [aut, cre], Brady Johnston [aut], Jakob Petereit [aut]

crosshap_1.4.0.tar.gz
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crosshap.pdf |crosshap.html✨
crosshap/json (API)

# Install 'crosshap' in R:

install.packages('crosshap', repos = c('https://bradyajohnston.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jacobimarsh/crosshap/issues

Pkgdown site:https://jacobimarsh.github.io

Datasets:

HapObject - Example Haplotype object
LD - Example LD matrix
metadata - Example Domestication metadata
pheno - Example phenotype data
vcf - Example VCF

On CRAN:

4.56 score 12 stars 4 scripts 303 downloads 22 exports 70 dependencies

Last updated 4 months agofrom:c31a82bb8d. Checks:8 OK. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 02 2025
R-4.5-win	OK	Feb 02 2025
R-4.5-mac	OK	Feb 02 2025
R-4.5-linux	OK	Feb 02 2025
R-4.4-win	OK	Feb 02 2025
R-4.4-mac	OK	Feb 02 2025
R-4.3-win	OK	Feb 02 2025
R-4.3-mac	OK	Feb 02 2025

Exports:%>%arith_mode build_bot_halfeyeplot build_left_alleleplot build_left_posplot build_mid_dotplot build_right_clusterplot build_right_phenoplot build_summary_tables build_top_metaplot clustree_viz crosshap_viz mean_na.rm prepare_hap_umap pseudo_haps read_LD read_metadata read_pheno read_vcf run_haplotyping run_hdbscan_haplotyping tagphenos

Dependencies:backports cachem checkmate cli clustree colorspace cpp11 data.table dbscan distributional dplyr fansi farver fastmap generics ggdist ggforce ggplot2 ggpp ggraph ggrepel glue graphlayouts gridExtra gtable igraph isoband jsonlite labeling lattice lifecycle lubridate magrittr MASS Matrix memoise mgcv munsell nlme numDeriv patchwork pillar pkgconfig polyclip polynom purrr quadprog R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang scales stringi stringr systemfonts tibble tidygraph tidyr tidyselect timechange tweenr utf8 vctrs viridis viridisLite withr xts zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mode utility function	arith_mode
Bot hap-pheno raincloud plot	build_bot_halfeyeplot
Left SNP-allele plot	build_left_alleleplot
Left SNP-position plot	build_left_posplot
Middle MG/hap dot plot	build_mid_dotplot
Right intra-cluster linkage plot	build_right_clusterplot
Right SNP-pheno phenoplot	build_right_phenoplot
Hap/MG summary tables	build_summary_tables
Top metadata-hap bar plot	build_top_metaplot
Clustering tree	clustree_viz
Visualize haplotypes	crosshap_viz
Example Haplotype object	HapObject
Example LD matrix	LD
Mean utility function	mean_na.rm
Example Domestication metadata	metadata
Example phenotype data	pheno
UMAP haplotype visualization helper	prepare_hap_umap
Identify haplotypes from clustered SNPs	pseudo_haps
Read LD correlation matrix to tibble	read_LD
Read metadata to tibble	read_metadata
Read phenotype data to tibble	read_pheno
Read VCF to tibble	read_vcf
Cluster SNPs and identify haplotypes	run_haplotyping
Cluster SNPs with HDBSCAN and identify haplotypes	run_hdbscan_haplotyping
Calculate SNP phenotypic associations	tagphenos
Example VCF	vcf